make[2]: Entering directory `/home/anwesha/amber14/AmberTools/test' ./test_at_clean.sh cd mmpbsa_py && make -k clean make[3]: Entering directory `/home/anwesha/amber14/AmberTools/test/mmpbsa_py' cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 02_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 03_Alanine_Scanning && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 04_Per_Residue_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 05_Pairwise_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 06_NAB_Nmode && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 07_Comprehensive && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 08_Stability && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 09_APBS_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 10_QM_MMGBSA && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 11_3D-RISM && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv make[3]: Leaving directory `/home/anwesha/amber14/AmberTools/test/mmpbsa_py' cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.clean cd ../src/FEW/examples/test && ./Run.few.clean cd cpptraj && make -k clean make[3]: Entering directory `/home/anwesha/amber14/AmberTools/test/cpptraj' Cleaning all test directories: (find . -name 'test.out' -o -name 'valgrind.out' -o -name 'Thread.*' \ -o -name 'Test_Results.dat' -o -name 'Test_Error.dat' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) make test.complete OPT=clean make[4]: Entering directory `/home/anwesha/amber14/AmberTools/test/cpptraj' make[4]: Leaving directory `/home/anwesha/amber14/AmberTools/test/cpptraj' make[3]: Leaving directory `/home/anwesha/amber14/AmberTools/test/cpptraj' cd leap/glycam/06j && ./Run.glycam clean cd leap/glycam/06EPb && ./Run.glycam clean cd leap/glycam/06j_10 && ./Run.glycam clean cd leap/glycam/06j_12SB && ./Run.glycam clean cd nab && make -k test testrism make[3]: Entering directory `/home/anwesha/amber14/AmberTools/test/nab' Running test to make dna duplex: diffing d01.pdb.check with d01.pdb PASSED ============================================================== Running test to computed 3DNA deformation energies: diffing deform.out.check with deform.out PASSED ============================================================== Running Reflexive test: diffing ref.out.check with ref.out PASSED ============================================================== Running test of sub() and gsub() diffing gsub_test.out.check with gsub_test.out PASSED ============================================================== Running test of hashed arrays: diffing hash.out.check with hash.out PASSED ============================================================== Running test to compute chemical shifts (this tests many parts of the compiler and libraries) diffing 5pti.shifts.check with 5pti.shifts PASSED ============================================================== Running test to do simple minimization (this tests the molecular mechanics interface) diffing ltest.out.check with ltest.out PASSED ============================================================== Running test to do simple minimization with shake (this tests the molecular mechanics interface) diffing rattle_min.out.check with rattle_min.out PASSED ============================================================== Running test of fibre-diffraction module diffing fd.pdb.check with fd.pdb PASSED ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing gbrna.out.check with gbrna.out PASSED ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing xfin_sa.out.check with xfin_sa.out PASSED ============================================================== Running test to do simple minimization (this tests the LCPO surface area) diffing gbrna_sa.out.check with gbrna_sa.out PASSED ============================================================== Running test to do simple minimization (this tests the ao generalized Born implementation) diffing gbtrx.out.check with gbtrx.out PASSED ============================================================== Running test to do simple minimization (this tests the ao-2 generalized Born implementation) diffing gb5trx.out.check with gb5trx.out PASSED ============================================================== Running test to do simple minimization (this tests the GB Neck implementation; gb==8) diffing gb8trx.out.check with gb8trx.out PASSED ============================================================== Running test to do simple minimization (this tests the GB Neck implementation; gb==7) diffing gb7trx.out.check with gb7trx.out PASSED ============================================================== Running test to do molecular dynamics with rattle diffing rattle_md.out.check with rattle_md.out PASSED ============================================================== Running test of randomized embedding diffing rembed.out.check with rembed.out PASSED ============================================================== Running test to compute NAB energy of 3dfr minus waters. Compare the NAB energy with the previously computed Amber energy: Amber8 total energy is 5184.0880 NAB total energy is 5184.0880 diffing dhfrndpmtx.out.check with dhfrndpmtx.out PASSED ============================================================== Running test to compute GB Newton-Raphson and normal modes: Note: Very small differences between asp.out and the saved file are common and do not necessarily indicate a problem. diffing asp.out.check with asp.out PASSED ============================================================== Running test to compute non-GB Newton-Raphson and normal modes: Note: Small differences are common and do not necessarily indicate a problem. diffing aspnb.out.check with aspnb.out PASSED ============================================================== Running test to create Amber force-field description diffing prm.out.check with prm.out PASSED ============================================================== checking the prmtop file: diffing tprmtop.check with tprmtop PASSED ============================================================== Running test to create a simple mmCIF file Formal charge is 0 Name is (2R)-3,3-dimethylbutan-2-amine diffing gbrna.cif.check with gbrna.cif PASSED ============================================================== diffing gbrna.pdb with gbrna2.pdb PASSED ============================================================== diffing component.00D.pdb.check with component.00D.pdb PASSED ============================================================== diffing 1BNA2.pdb.check with 1BNA2.pdb PASSED ============================================================== Running test to do simple xmin minimization diffing txmin.out.check with txmin.out PASSED ============================================================== Running test on netcdf files diffing tnetcdf.out.check with tnetcdf.out PASSED ============================================================== Running test for variable 1-4 scaled nonbonded interactions diffing variable_14scale.out.check with variable_14scale.out PASSED ============================================================== Running test to do simple lmod optimization diffing tlmod.out.check with tlmod.out PASSED ============================================================== Running test to compute GB normal modes using DSYEVD: diffing asp_nm1.out.check with asp_nm1.out PASSED ============================================================== Running test to compute GB normal modes using DSAUPD: diffing asp_nm2.out.check with asp_nm2.out PASSED ============================================================== Running test to compute Langevin modes: diffing asp_nm3.out.check with asp_nm3.out PASSED ============================================================== Running test of the isotropic periodic sum technique diffing dhfr_ips.out.check with dhfr_ips.out PASSED ============================================================== Running test to do simple minimization (libpbsa) (this tests the PBSA implementation) diffing pbdmp.out.check with pbdmp.out PASSED ============================================================== Running test to do simple minimization (librism) (this tests the 3D-RISM implementation) diffing rismdmp.out.check with rismdmp.out PASSED ============================================================== Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) diffing rismala.out.check with rismala.out PASSED ============================================================== Running test to do basic MD (librism) (this tests the 3D-RISM-KH precission) diffing rismdist.out.check with rismdist.out PASSED ============================================================== diffing guv.O.4.dx.check with guv.O.4.dx PASSED ============================================================== diffing guv_dT.O.4.dx.check with guv_dT.O.4.dx PASSED ============================================================== diffing huv.O.4.dx.check with huv.O.4.dx PASSED ============================================================== diffing cuv.O.4.dx.check with cuv.O.4.dx PASSED ============================================================== diffing cuv_dT.O.4.dx.check with cuv_dT.O.4.dx PASSED ============================================================== diffing guv.H1.4.dx.check with guv.H1.4.dx PASSED ============================================================== diffing guv_dT.H1.4.dx.check with guv_dT.H1.4.dx PASSED ============================================================== diffing huv.H1.4.dx.check with huv.H1.4.dx PASSED ============================================================== diffing cuv.H1.4.dx.check with cuv.H1.4.dx PASSED ============================================================== diffing cuv_dT.H1.4.dx.check with cuv_dT.H1.4.dx PASSED ============================================================== diffing quv.4.dx.check with quv.4.dx PASSED ============================================================== diffing chgdist.4.dx.check with chgdist.4.dx PASSED ============================================================== diffing exchem.H1.4.dx.check with exchem.H1.4.dx PASSED ============================================================== diffing solvene.H1.4.dx.check with solvene.H1.4.dx PASSED ============================================================== diffing entropy.H1.4.dx.check with entropy.H1.4.dx PASSED ============================================================== diffing exchemGF.H1.4.dx.check with exchemGF.H1.4.dx PASSED ============================================================== diffing solveneGF.H1.4.dx.check with solveneGF.H1.4.dx PASSED ============================================================== diffing entropyGF.H1.4.dx.check with entropyGF.H1.4.dx PASSED ============================================================== diffing exchem.O.4.dx.check with exchem.O.4.dx PASSED ============================================================== diffing solvene.O.4.dx.check with solvene.O.4.dx PASSED ============================================================== diffing entropy.O.4.dx.check with entropy.O.4.dx PASSED ============================================================== diffing exchemGF.O.4.dx.check with exchemGF.O.4.dx PASSED ============================================================== diffing solveneGF.O.4.dx.check with solveneGF.O.4.dx PASSED ============================================================== diffing entropyGF.O.4.dx.check with entropyGF.O.4.dx PASSED ============================================================== diffing exchem.4.dx.check with exchem.4.dx PASSED ============================================================== diffing solvene.4.dx.check with solvene.4.dx PASSED ============================================================== diffing entropy.4.dx.check with entropy.4.dx PASSED ============================================================== diffing exchemGF.4.dx.check with exchemGF.4.dx PASSED ============================================================== diffing solveneGF.4.dx.check with solveneGF.4.dx PASSED ============================================================== diffing entropyGF.4.dx.check with entropyGF.4.dx PASSED ============================================================== diffing potUV.H1.4.dx.check with potUV.H1.4.dx PASSED ============================================================== diffing potUV.O.4.dx.check with potUV.O.4.dx PASSED ============================================================== diffing potUV.4.dx.check with potUV.4.dx PASSED ============================================================== Running test to do basic MD (librism) (this tests the 3D-RISM-HNC implementation) diffing rismhnc.out.check with rismhnc.out PASSED ============================================================== Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) diffing rismion.out.check.totChg with rismion.out.totChg PASSED ============================================================== diffing rismion.out.check.rel with rismion.out.rel PASSED ============================================================== Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) diffing rismala-nocut.out.check with rismala-nocut.out PASSED ============================================================== Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) diffing rismala-pse1.out.check with rismala-pse1.out PASSED ============================================================== Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) diffing rismion.noasymp.out.check.totChg with rismion.noasymp.out.totChg PASSED ============================================================== diffing rismion.noasymp.out.check.rel with rismion.noasymp.out.rel PASSED ============================================================== Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) diffing rismion_pse1.out.check.totChg with rismion_pse1.out.totChg PASSED ============================================================== diffing rismion_pse1.out.check.rel with rismion_pse1.out.rel PASSED ============================================================== Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) diffing rismion_pse3.out.check.totChg with rismion_pse3.out.totChg PASSED ============================================================== diffing rismion_pse3.out.check.rel with rismion_pse3.out.rel PASSED ============================================================== Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) diffing rismala-mdiis0.out.check with rismala-mdiis0.out PASSED ============================================================== Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) diffing rismala-mdiis1.out.check with rismala-mdiis1.out PASSED ============================================================== Running test for 3D-RISM closure list (librism) (testing mm_options parsing) diffing rismlist.out.check with rismlist.out PASSED ============================================================== Running test to do basic MD (librism) (trajectory processing using the 3D-RISM command line interface) /home/anwesha/amber14/bin/rism3d.snglpnt diffing rism3d.snglpnt.out.check.totChg with rism3d.snglpnt.out.totChg PASSED ============================================================== diffing rism3d.snglpnt.out.check.rel with rism3d.snglpnt.out.rel PASSED ============================================================== diffing quv.1.xyzv.trunc.check with quv.1.xyzv.trunc PASSED ============================================================== diffing quv.2.xyzv.trunc.check with quv.2.xyzv.trunc PASSED ============================================================== diffing quv.3.xyzv.trunc.check with quv.3.xyzv.trunc PASSED ============================================================== Running test to do basic MD (librism) (trajectory processing version 2 using the 3D-RISM command line interface) diffing rism3d.snglpnt.2.out.check.totChg with rism3d.snglpnt.2.out.totChg PASSED ============================================================== diffing rism3d.snglpnt.2.out.check.rel with rism3d.snglpnt.2.out.rel PASSED ============================================================== diffing guv.2.O.1.dx.check with guv.2.O.1.dx PASSED ============================================================== diffing guv.2.H1.2.dx.check with guv.2.H1.2.dx PASSED ============================================================== diffing guv.2.O.3.dx.check with guv.2.O.3.dx PASSED ============================================================== Running test for 3D-RISM closure list (librism) (trajectory processing test) /home/anwesha/amber14/bin/rism3d.snglpnt diffing rism3d.snglpnt.list.out.check.totChg with rism3d.snglpnt.list.out.totChg PASSED ============================================================== diffing rism3d.snglpnt.list.out.check.rel with rism3d.snglpnt.list.out.rel PASSED ============================================================== Running test to do simple minimization (librism) (this tests the 3D-RISM implementation) diffing rismxmin.out.check.totChg with rismxmin.out.totChg PASSED ============================================================== diffing rismxmin.out.check.rel with rismxmin.out.rel PASSED ============================================================== diffing ala.rismxmin.pdb.check with ala.rismxmin.pdb PASSED ============================================================== diffing g.xmin.O.0.dx.check with g.xmin.O.0.dx PASSED ============================================================== make[3]: Leaving directory `/home/anwesha/amber14/AmberTools/test/nab' cd cpptraj && make -k test make[3]: Entering directory `/home/anwesha/amber14/AmberTools/test/cpptraj' make test.main make[4]: Entering directory `/home/anwesha/amber14/AmberTools/test/cpptraj' ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_General CPPTRAJ: General tests diffing distance.dat.save with distance.dat PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing rmsda.dat.save with rmsda.dat PASSED ============================================================== diffing phi2.dat.save with phi2.dat PASSED ============================================================== diffing PhiPsi.dat.save with PhiPsi.dat PASSED ============================================================== diffing test.crd.save with test.crd PASSED ============================================================== diffing a1.dat.save with a1.dat PASSED ============================================================== diffing test.rst7.213.save with Restart/test.rst7.213 PASSED ============================================================== diffing nc0 with nc1 PASSED ============================================================== diffing r4.dat.save with r4.dat PASSED ============================================================== diffing a2.dat.gz.save with a2.dat.gz PASSED ============================================================== diffing a3.dat.bz2.save with a3.dat.bz2 PASSED ============================================================== diffing r2.dat.save with r2.dat PASSED ============================================================== diffing r3-nofit.dat.save with r3-nofit.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Strip CPPTRAJ: One frame strip command test. diffing dummy.pdb.save with dummy.pdb PASSED ============================================================== diffing dummy.rst7.save with dummy.rst7 PASSED ============================================================== diffing strip.tz2.truncoct.parm7.save with strip.tz2.truncoct.parm7 PASSED ============================================================== CPPTRAJ: Unstrip (Lig/Rec/Complex) command test. diffing strip.tz2.truncoct.parm7.save with complex.tz2.truncoct.parm7 PASSED ============================================================== diffing receptor.tz2.truncoct.parm7.save with receptor.tz2.truncoct.parm7 PASSED ============================================================== diffing ligand.tz2.truncoct.parm7.save with ligand.tz2.truncoct.parm7 PASSED ============================================================== diffing Ligand.crd.save with Ligand.crd PASSED ============================================================== diffing Receptor.crd.save with Receptor.crd PASSED ============================================================== diffing Complex.crd.save with Complex.crd PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Broken Traj: Running broken trajectory. diffing goodrmsd.dat with badrmsd.dat PASSED ============================================================== CPPTRAJ: Broken Traj: Running compressed broken trajectory. diffing goodrmsd.dat with ziprmsd.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_TrajinOffset CPPTRAJ: Normal trajectory read with offsets. diffing rem.crd.save with rem.crd.combined PASSED ============================================================== CPPTRAJ: Gzipped trajectory read with offsets. diffing rem.crd.save with gzip.rem.crd.combined PASSED ============================================================== CPPTRAJ: Bzip2ed trajectory read with offsets. diffing rem.crd.save with bzip2.rem.crd.combined PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_RemdTraj CPPTRAJ: CRD Replica Trajectory Run with offset diffing d1.offset.dat.save with d1.offset.dat PASSED ============================================================== CPPTRAJ: CRD Replica Trajectory Run diffing d1.crd.dat.save with d1.crd.dat PASSED ============================================================== CPPTRAJ: NETCDF Replica Trajectory Run diffing d1.nc.dat.save with d1.nc.dat PASSED ============================================================== CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: CRD Replica Trajectory Run with remdout diffing d1.ensemble.dat.save with d1.ensemble.dat PASSED ============================================================== diffing temp0.crd.300.00 with temp.crd.0 PASSED ============================================================== diffing temp0.crd.384.30 with temp.crd.1 PASSED ============================================================== diffing temp0.crd.492.20 with temp.crd.2 PASSED ============================================================== diffing temp0.crd.630.50 with temp.crd.3 PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] diffing test.rst7.3.save with test.rst7.3 PASSED ============================================================== diffing test.rst7.5.save with test.rst7.5 PASSED ============================================================== diffing test.rst7.6.save with test.rst7.6 PASSED ============================================================== diffing test.rst7.7.save with test.rst7.7 PASSED ============================================================== diffing test.rst7.8.save with test.rst7.8 PASSED ============================================================== CPPTRAJ: Trajout Frame Range [Amber Coordinates] diffing framerange.crd.save with framerange.crd PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. diffing PerResRMSD.agr.save with PerResRMSD.agr PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with averaging. diffing perresavg.dat.save with perresavg.dat PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with residue centering. diffing center.agr.save with center.agr PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. diffing dssp.gnu.save with dssp.gnu PASSED ============================================================== diffing dssp.sum.agr.save with dssp.sum.agr PASSED ============================================================== CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. diffing dssp.dat.save with dssp.dat PASSED ============================================================== diffing dssp.dat.sum.save with dssp.dat.sum PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Hbond CPPTRAJ: Solute Hbond test. diffing nhb.dat.save with nhb.dat PASSED ============================================================== diffing avghb.dat.save with avghb.dat PASSED ============================================================== CPPTRAJ: Solvent Hbond test. diffing solvhb.dat.save with solvhb.dat PASSED ============================================================== diffing solvavg.dat.save with solvavg.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: NetCDF Restart Test - NetCDF->TXT diffing ../tz2.rst7 with text.rst7 PASSED ============================================================== CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt diffing ../tz2.ortho.rst7 with text.rst7 PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Image CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: Non-orthorhombic imaged distance test. diffing ortho.dat.save with ortho.dat PASSED ============================================================== diffing nonortho.dat.save with nonortho.dat PASSED ============================================================== CPPTRAJ: Orthorhombic coordinate imaging test. CPPTRAJ: Nonorthorhombic coordinate imaging test. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM. diffing image.crd.save with image.crd PASSED ============================================================== diffing image2.crd.save with image2.crd PASSED ============================================================== diffing image3.crd.save with image3.crd PASSED ============================================================== diffing image4.crd.save with image4.crd PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Surf CPPTRAJ: Surface calculation test. diffing surf.dat.save with surf.dat PASSED ============================================================== CPPTRAJ: Partial Surface calculation test. diffing tsurf.dat.save with tsurf.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Radgyr CPPTRAJ: Radius of gyration command test. diffing radgyr.dat.save with radgyr.dat PASSED ============================================================== diffing radgyr.mass.dat.save with radgyr.mass.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Mask CPPTRAJ: Mask command test. diffing mask.out.save with mask.out PASSED ============================================================== diffing mask.pdb.1.save with mask.pdb.1 PASSED ============================================================== diffing mask.mol2.1.save with mask.mol2.1 PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing T1.crd with T2.crd PASSED ============================================================== diffing ../tz2.truncoct.crd with test.crd PASSED ============================================================== CPPTRAJ: Outtraj Test with filtering. diffing maxmin.crd.save with maxmin.crd PASSED ============================================================== CPPTRAJ: Outtraj Test with maxmin. diffing maxmin.crd.save with maxmin.crd PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Charmm CPPTRAJ: CHARMM PSF/DCD test diffing test.ala3.pdb.save with test.ala3.pdb PASSED ============================================================== CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: CHARMM DCD Write, step 2. diffing first.ala3.crd with second.ala3.crd PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Rotdif CPPTRAJ: Rotdif test diffing rvecs.dat.save with rvecs.dat PASSED ============================================================== diffing matrices.dat.save with matrices.dat PASSED ============================================================== diffing deffs.dat.save with deffs.dat PASSED ============================================================== diffing rotdif.out.save with rotdif.out PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Runavg CPPTRAJ: Coordinate Running Average diffing runavg.crd.save with runavg.crd PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_2DRMS CPPTRAJ: 2D RMSD Test. diffing rmsd.dat.save with rmsd2.dat PASSED ============================================================== CPPTRAJ: 2D RMSD Test, mass-weighted. diffing rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== CPPTRAJ: 2D RMSD Test with reference trajectory. diffing rmsd.dat.save with rmsd1.dat PASSED ============================================================== CPPTRAJ: 2D DME Test. diffing dme.dat.save with dme.dat PASSED ============================================================== CPPTRAJ: 2D RMSD with reference mask test. diffing trp.dat.save with trp.dat PASSED ============================================================== CPPTRAJ: 2D RMSD test, no fitting. diffing nofit.dat.save with nofit.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. diffing L01.mol2.1.save with L01.mol2 PASSED ============================================================== diffing tz2.mol2.1.save with tz2.mol2 PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_NAstruct CPPTRAJ: NAstruct command test. diffing BP.adh026.dat.save with BP.adh026.dat PASSED ============================================================== diffing BPstep.adh026.dat.save with BPstep.adh026.dat PASSED ============================================================== diffing Helix.adh026.dat.save with Helix.adh026.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Average CPPTRAJ: Average Test. diffing test.pdb.save with test.pdb PASSED ============================================================== diffing test.pdb.save with test2.pdb PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Pucker CPPTRAJ: Pucker command test diffing pucker.dat.save with pucker.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_AtomMap CPPTRAJ: AtomMap Test diffing initial.mol2.save with initial.mol2 PASSED ============================================================== diffing atommap.dat.save with atommap.dat PASSED ============================================================== diffing reordered.pdb.save with reordered.pdb PASSED ============================================================== diffing reordered.mol2.save with reordered.mol2 PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing fit.mol2.save with fit.mol2 PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Datafile CPPTRAJ: Data file output precision test. diffing prec.dat.save with prec.dat PASSED ============================================================== CPPTRAJ: Standard -> Grace Data CPPTRAJ: Grace -> Standard Data diffing ../Test_General/a1.dat.save with a1.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Radial CPPTRAJ: Radial Test diffing Radial.agr.save with Radial.agr PASSED ============================================================== diffing cRadial.agr.save with cRadial.agr PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Hist CPPTRAJ: Histogram Analysis Test diffing hist.gnu.save with hist.gnu PASSED ============================================================== diffing hist.agr.save with hist.agr PASSED ============================================================== diffing freeE.gnu.save with freeE.gnu PASSED ============================================================== diffing norm.gnu.save with norm.gnu PASSED ============================================================== CPPTRAJ: 3D histogram test. diffing hist.dx.save with hist.dx PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Closest CPPTRAJ: Closest command test using first solvent atom. diffing first.Closest.pdb.save with first.Closest.pdb PASSED ============================================================== diffing closestmols.dat.save with closestmols.dat PASSED ============================================================== diffing closest.tz2.truncoct.parm7.save with closest.tz2.truncoct.parm7 PASSED ============================================================== CPPTRAJ: Closest command test using all solvent atoms. diffing all.Closest.pdb.save with all.Closest.pdb PASSED ============================================================== CPPTRAJ: Closest command test using mask center. diffing center.closest.pdb.save with center.closest.pdb PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_DRMSD CPPTRAJ: Distance RMSD test. diffing drmsd.dat.save with drmsd.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Cluster CPPTRAJ: Cluster command test. diffing cnumvtime.dat.save with cnumvtime.dat PASSED ============================================================== diffing avg.summary.dat.save with avg.summary.dat PASSED ============================================================== diffing summary.dat.save with summary.dat PASSED ============================================================== diffing cpop.agr.save with cpop.agr PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_CheckStructure CPPTRAJ: Structure Check diffing report.dat.save with report.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference diffing rmscorr.dat.save with rmscorr.dat PASSED ============================================================== diffing rmscorr.10.dat.save with rmscorr.10.dat PASSED ============================================================== CPPTRAJ: RmsAvgCorr First diffing rmscorr.first.dat.save with rmscorr.first.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Vector CPPTRAJ: Vector Tests diffing vtest.dat.0.save with vtest.dat.0 PASSED ============================================================== diffing vtest.dat.1.save with vtest.dat.1 PASSED ============================================================== diffing vtest.dat.2.save with vtest.dat.2 PASSED ============================================================== diffing vtest.dat.3.save with vtest.dat.3 PASSED ============================================================== diffing vtest.dat.4.save with vtest.dat.4 PASSED ============================================================== diffing vtest.dat.5.save with vtest.dat.5 PASSED ============================================================== diffing vtest.dat.6.save with vtest.dat.6 PASSED ============================================================== diffing vtest.dat.7.save with vtest.dat.7 PASSED ============================================================== diffing v8.mol2.save with v8.mol2 PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_AtomicFluct CPPTRAJ: Cpptraj: Atomic fluctuations test [@C,CA,N byres bfactor]. diffing fluct.1.dat.save with fluct.1.dat PASSED ============================================================== CPPTRAJ: Cpptraj: Atomic fluctuations test [:2-12 byatom]. diffing fluct.2.dat.save with fluct.2.dat PASSED ============================================================== CPPTRAJ: Cpptraj: Atomic fluctuations test [bymask :3,4,5]. diffing fluct.3.dat.save with fluct.3.dat PASSED ============================================================== CPPTRAJ: Cpptraj: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. diffing fluct.4.dat.save with fluct.4.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Grid CPPTRAJ: Dipole test diffing out.dipole.save with out.dipole PASSED ============================================================== CPPTRAJ: Grid test diffing out.xplor.save with out.xplor PASSED ============================================================== diffing out.dx.save with out.dx PASSED ============================================================== CPPTRAJ: OpenDX Grid read test diffing out.dx.save with out.dx.2 PASSED ============================================================== CPPTRAJ: Grid with specified center test. diffing test.dx.save with test.dx PASSED ============================================================== CPPTRAJ: Grid with box center offset test. diffing box.dx.save with box.dx PASSED ============================================================== CPPTRAJ: Grid with mask center offset test. diffing mask.dx.save with mask.dx PASSED ============================================================== CPPTRAJ: Non-orthogonal grid test. diffing nonortho.dx.save with nonortho.dx PASSED ============================================================== CPPTRAJ: Grid generationg from bounds test. diffing bounds.dat.save with bounds.dat PASSED ============================================================== diffing bounds.xplor.save with bounds.xplor PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Watershell CPPTRAJ: Watershell Test diffing ws.agr.save with ws.agr PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average diffing running_avg.dat.save with running_avg.dat PASSED ============================================================== diffing cumulative_avg.dat.save with cumulative_avg.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_Density CPPTRAJ: Density Test. diffing number_density.dat.save with number_density.dat PASSED ============================================================== diffing mass_density.dat.save with mass_density.dat PASSED ============================================================== diffing charge_density.dat.save with charge_density.dat PASSED ============================================================== diffing electron_density.dat.save with electron_density.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. diffing sn1_est.dat.save with sn1_est.dat PASSED ============================================================== diffing e2e_sn1.dat.save with e2e_sn1.dat PASSED ============================================================== diffing sn2_est.dat.save with sn2_est.dat PASSED ============================================================== diffing e2e_sn2.dat.save with e2e_sn2.dat PASSED ============================================================== diffing sn1_dir.dat.save with sn1_dir.dat PASSED ============================================================== diffing sn2_dir.dat.save with sn2_dir.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_PairDist CPPTRAJ: PairDist Test. diffing Pr.dat.save with Pr.dat PASSED ============================================================== ************************************************************** TEST: /home/anwesha/amber14/AmberTools/test/cpptraj/Test_AmbPDB | ambpdb (C++) Version V15.00 diffing out.pdb.save with out.pdb PASSED ============================================================== | ambpdb (C++) Version V15.00 | Reading Amber restart from STDIN diffing out.pdb.save with out.pdb PASSED ============================================================== make[4]: Leaving directory `/home/anwesha/amber14/AmberTools/test/cpptraj' make[3]: Leaving directory `/home/anwesha/amber14/AmberTools/test/cpptraj' cd antechamber/bondtype && ./Run.bondtype diffing ABAKOE.prepi.save with ABAKOE.prepi PASSED ============================================================== diffing PFPHHG02.prepi.save with PFPHHG02.prepi PASSED ============================================================== diffing fluorescein2.mol2.save with fluorescein2.mol2 PASSED ============================================================== diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2 PASSED ============================================================== cd antechamber/c60 && ./Run.c60 diffing buckyball.mol2.save with buckyball.mol2 PASSED ============================================================== diffing buckyball.gzmat.save with buckyball.gzmat PASSED ============================================================== diffing buckyball.jcrt.save with buckyball.jcrt PASSED ============================================================== diffing buckyball.prepi.save with buckyball.prepi PASSED ============================================================== diffing buckyball.ac.save with buckyball.ac PASSED ============================================================== cd antechamber/charmm && ./Run.charmm diffing ala2.inp.save with ala2.inp PASSED ============================================================== diffing ala2.rtf.save with ala2.rtf PASSED ============================================================== diffing ala2.prm.save with ala2.prm PASSED ============================================================== diffing ala2_charmm.mol2.save with ala2_charmm.mol2 PASSED ============================================================== cd antechamber/chemokine && ./Run.1b2t diffing 1b2t.mol2.save with 1b2t.mol2 PASSED ============================================================== diffing 1b2t.ac.save with 1b2t.ac PASSED ============================================================== cd antechamber/tp && ./Run.tp diffing tp.mol2.save with tp.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing frcmod.full.save with frcmod.full PASSED ============================================================== cd antechamber/ash && ./Run.ash diffing ash.mol2.save with ash.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/sustiva && ./Run.sustiva diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out PASSED ============================================================== diffing prmtop.save with prmtop PASSED ============================================================== cd antechamber/fluorescein && ./Run.fluorescein diffing fluorescein.mol2.save with fluorescein.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/guanine_amber && ./Run.guanine_amber diffing DGN.mol2.save with DGN.mol2 PASSED ============================================================== cd antechamber/fpph && ./Run.fpph_resp diffing fpph_resp.mol2.save with fpph_resp.mol2 PASSED ============================================================== cd antechamber/residuegen && ./Run.ala diffing ala.ac.save with ala.ac PASSED ============================================================== diffing ala.esp.save with ala.esp PASSED ============================================================== diffing ala.prep.save with ala.prep PASSED ============================================================== cd antechamber/parmchk2 && ./Run.parmchk2 diffing ccl3br.frcmod.save with ccl3br.frcmod PASSED ============================================================== diffing diethylamine.frcmod.save with diethylamine.frcmod PASSED ============================================================== diffing N-methylacetamide.frcmod.save with N-methylacetamide.frcmod PASSED ============================================================== cd mdgx/1p7e && ./Test.1p7e diffing energy.dat.save with energy.dat PASSED ============================================================== cd mdgx/NVTwat && ./Test.nvtwat diffing temperature.dat.save with temperature.dat PASSED ============================================================== cd mdgx/MLE && ./Test.mle diffing Eelec.dat.save with Eelec.dat PASSED ============================================================== cd mdgx/Settle && ./Test.settle diffing etot.dat.save with etot.dat PASSED ============================================================== cd mdgx/MCBarostat && ./Test.mcb diffing vol.dat.save with vol.dat PASSED ============================================================== cd mdgx/TIP4P && ./Test.tip4p diffing temperature.dat.save with temperature.dat PASSED ============================================================== cd mdgx/ForceCalc && ./Test.frcc diffing frceval.dat.save with frceval.dat PASSED ============================================================== cd mdgx/AddEP && ./Test.addep diffing etot.dat.save with etot.dat PASSED ============================================================== cd mdgx/QFit && ./Test.qfit diffing hydrogenQ.dat.save with hydrogenQ.dat PASSED ============================================================== diffing fqpt.dat.save with fqpt.dat PASSED ============================================================== cd mdgx/Triclinic && ./Test.triclinic diffing temperature.dat.save with temperature.dat PASSED ============================================================== cd leap && ./Run.tleap AMBERHOME is set to /home/anwesha/amber14 Running leap tests on ./tleap -> ../../bin/teLeap building force field libraries: '94 ff.. diffing /home/anwesha/amber14/dat/leap/lib/all_amino94.lib with all_amino94.lib PASSED ============================================================== diffing /home/anwesha/amber14/dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib PASSED ============================================================== diffing /home/anwesha/amber14/dat/leap/lib/all_aminont94.lib with all_aminont94.lib PASSED ============================================================== diffing /home/anwesha/amber14/dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib PASSED ============================================================== diffing /home/anwesha/amber14/dat/leap/lib/ions94.lib with ions94.lib PASSED ============================================================== loadpdb and saveamberparm: 94 ff.. - aminoan94 comparing topology to earlier leap version.. diffing ff94/all_aminoan94.top with all_aminoan94.top PASSED ============================================================== - aminonc94 comparing topology to earlier leap version.. diffing ff94/all_aminonc94.top with all_aminonc94.top PASSED ============================================================== - dna94 comparing topology to earlier leap version.. diffing ff94/all_dna94.top with all_dna94.top PASSED ============================================================== - rna94 comparing topology to earlier leap version.. diffing ff94/all_rna94.top with all_rna94.top PASSED ============================================================== -------------------------------------------------------------- Notes: - If all tests PASSED, you can 'rm *.log *.out *.lib *.top' - For a discussion of energy differences (sander*.dif) see 0README. - It is common to see round-off differences in the portion of these tests -------------------------------------------------------------- cd leap && ./Run.parm7 Creating a new-style (Amber 7) topology file diffing trx.parm7.save with trx.parm7 PASSED ============================================================== diffing trx.solv.parm7.save with trx.solv.parm7 PASSED ============================================================== cd leap && ./Run.cmds Test of several LEaP features diffing sys1.mbondi2.parm7.save with sys1.mbondi2.parm7 PASSED ============================================================== diffing sys2.mbondi2.parm7.save with sys2.mbondi2.parm7 PASSED ============================================================== diffing sys1.mbondi2.rst7.save with sys1.mbondi2.rst7 PASSED ============================================================== diffing sys1_sys2.mbondi.parm7.save with sys1_sys2.mbondi.parm7 PASSED ============================================================== diffing sys1_sys2.mbondi.rst7.save with sys1_sys2.mbondi.rst7 PASSED ============================================================== diffing d_glu.bondi.parm7.save with d_glu.bondi.parm7 PASSED ============================================================== diffing d_glu.bondi.rst7.save with d_glu.bondi.rst7 PASSED ============================================================== cd leap && ./Run.mbondi3 Creating a new-style (Amber 7) topology file with mbondi3 diffing alphabet.mbondi3.parm7.save with alphabet.mbondi3.parm7 PASSED ============================================================== cd leap && ./Run.addions Checking that addIons neutralizes as well as possible diffing neg_lys_addions.parm7.save with neg_lys_addions.parm7 PASSED ============================================================== cd leap/glycam/06j && ./Run.glycam ** Testing prmtop and inpcrd built by tleap with GLYCAM_06j. ** diffing Branches.parm7.save with Branches.parm7 PASSED ============================================================== diffing Branches.rst7.save with Branches.rst7 PASSED ============================================================== diffing Chains.parm7.save with Chains.parm7 PASSED ============================================================== diffing Chains.rst7.save with Chains.rst7 PASSED ============================================================== diffing Derivatives.parm7.save with Derivatives.parm7 PASSED ============================================================== diffing Derivatives.rst7.save with Derivatives.rst7 PASSED ============================================================== diffing Solvate_Ion.parm7.save with Solvate_Ion.parm7 PASSED ============================================================== diffing Solvate_Ion.rst7.save with Solvate_Ion.rst7 PASSED ============================================================== cd leap/glycam/06EPb && ./Run.glycam ** Testing prmtop and inpcrd built by tleap with GLYCAM_06EPb. ** diffing EP.parm7.save with EP.parm7 PASSED ============================================================== diffing EP.rst7.save with EP.rst7 PASSED ============================================================== diffing Solvate.parm7.save with Solvate.parm7 PASSED ============================================================== diffing Solvate.rst7.save with Solvate.rst7 PASSED ============================================================== cd leap/glycam/06j_10 && ./Run.glycam ** Testing prmtop and inpcrd built by tleap with GLYCAM_06j_10. ** diffing Glycoprotein.parm7.save with Glycoprotein.parm7 PASSED ============================================================== diffing Glycoprotein.rst7.save with Glycoprotein.rst7 PASSED ============================================================== cd leap/glycam/06j_12SB && ./Run.glycam ** Testing prmtop and inpcrd built by tleap with GLYCAM_06j_12SB. ** diffing Glycoprotein.parm7.save with Glycoprotein.parm7 PASSED ============================================================== diffing Glycoprotein.rst7.save with Glycoprotein.rst7 PASSED ============================================================== cd resp && ./Run.ade RESP stage 1: diffing ade_1st.out.save with ade_1st.out PASSED ============================================================== diffing ade_1st.pch.save with ade_1st.pch PASSED ============================================================== diffing ade_1st_calc.esp.save with ade_1st_calc.esp PASSED ============================================================== RESP stage 2: diffing ade_1st.chg.save with ade_1st.chg PASSED ============================================================== diffing ade_2nd.out.save with ade_2nd.out PASSED ============================================================== diffing ade_2nd.pch.save with ade_2nd.pch PASSED ============================================================== diffing ade_2nd.chg.save with ade_2nd.chg PASSED ============================================================== cd pbsa_dmp && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== cd pbsa_p3m && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== cd pbsa_bcopt && ./Run.dmp.min bcoption=5 diffing bc5.mdout.dmp.min.save with bc5.mdout.dmp.min PASSED ============================================================== bcoption=6 diffing bc6.mdout.dmp.min.save with bc6.mdout.dmp.min PASSED ============================================================== bcoption=7 diffing bc7.mdout.dmp.min.save with bc7.mdout.dmp.min PASSED ============================================================== bcoption=9 diffing bc9.mdout.dmp.min.save with bc9.mdout.dmp.min PASSED ============================================================== cd pbsa_saopt && ./Run.dmp.min sasopt=0, saopt=-1 diffing sas0.sa-1.mdout.dmp.min.save with sas0.sa-1.mdout.dmp.min PASSED ============================================================== sasopt=0, saopt=-2 diffing sas0.sa-2.mdout.dmp.min.save with sas0.sa-2.mdout.dmp.min PASSED ============================================================== sasopt=1, saopt=-1 diffing sas1.sa-1.mdout.dmp.min.save with sas1.sa-1.mdout.dmp.min PASSED ============================================================== sasopt=1, saopt=-2 diffing sas1.sa-2.mdout.dmp.min.save with sas1.sa-2.mdout.dmp.min PASSED ============================================================== cd pbsa_tri && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== checking dmp force diffing force.save with force.dat PASSED ============================================================== cd pbsa_rot && ./Run.charge.min diffing mdout.charge.min.save with mdout.charge.min PASSED ============================================================== cd pbsa_lpb && ./Run.lsolver.min bcoption=1 solvopt=1 diffing out.save/mdout.min_bc1_solv1.save with mdout.min_bc1_solv1 PASSED ============================================================== bcoption=1 solvopt=2 diffing out.save/mdout.min_bc1_solv2.save with mdout.min_bc1_solv2 PASSED ============================================================== bcoption=1 solvopt=3 diffing out.save/mdout.min_bc1_solv3.save with mdout.min_bc1_solv3 PASSED ============================================================== bcoption=1 solvopt=4 diffing out.save/mdout.min_bc1_solv4.save with mdout.min_bc1_solv4 PASSED ============================================================== bcoption=5 solvopt=1 diffing out.save/mdout.min_bc5_solv1.save with mdout.min_bc5_solv1 PASSED ============================================================== bcoption=5 solvopt=2 diffing out.save/mdout.min_bc5_solv2.save with mdout.min_bc5_solv2 PASSED ============================================================== bcoption=5 solvopt=3 diffing out.save/mdout.min_bc5_solv3.save with mdout.min_bc5_solv3 PASSED ============================================================== bcoption=5 solvopt=4 diffing out.save/mdout.min_bc5_solv4.save with mdout.min_bc5_solv4 PASSED ============================================================== bcoption=10 solvopt=1 diffing out.save/mdout.min_bc10_solv1.save with mdout.min_bc10_solv1 PASSED ============================================================== bcoption=10 solvopt=2 diffing out.save/mdout.min_bc10_solv2.save with mdout.min_bc10_solv2 PASSED ============================================================== bcoption=10 solvopt=3 diffing out.save/mdout.min_bc10_solv3.save with mdout.min_bc10_solv3 PASSED ============================================================== bcoption=10 solvopt=4 diffing out.save/mdout.min_bc10_solv4.save with mdout.min_bc10_solv4 PASSED ============================================================== cd pbsa_tsr && ./Run.tsrb.min diffing mdout.tsrb.min.save with mdout.tsrb.min PASSED ============================================================== cd pbsa_radi && ./Run.ion.min diffing ./out.save/Na.inp1.out.save with Na.inp1.out PASSED ============================================================== diffing ./out.save/Na.inp2.out.save with Na.inp2.out PASSED ============================================================== diffing ./out.save/nma.inp1.out.save with nma.inp1.out PASSED ============================================================== diffing ./out.save/nma.inp2.out.save with nma.inp2.out PASSED ============================================================== diffing ./out.save/da.inp1.out.save with da.inp1.out PASSED ============================================================== diffing ./out.save/da.inp2.out.save with da.inp2.out PASSED ============================================================== cd pbsa_npb && ./test pbsa.ncg.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nsor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.asor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.dsor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.ntmg.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nticcg.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nticcg.bc6 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== cd pbsa_frc && ./test dbf_0.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_0.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_1.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_1.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_2.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_2.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_3.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_3.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== cd pbsa_ipb2 && ./Run.110D.min diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== cd pbsa_delphi && ./test working on ./Run.1az6.min diffing mdout.1az6.min.save with mdout.1az6.min PASSED ============================================================== working on ./Run.1az6.pqr diffing mdout.1az6.pqr.save with mdout.1az6.pqr PASSED ============================================================== cd pbsa_IIM && ./Run.IIM.min diffing mdout.min_bc6_solv2.save with mdout.min_bc6_solv2 PASSED ============================================================== diffing mdout.min_bc6_solv3.save with mdout.min_bc6_solv3 PASSED ============================================================== cd pbsa_ligand && ./Run.t4bnz.min diffing mdout.lig.min.save with mdout.lig.min PASSED ============================================================== cd pbsa_mbfocus && ./test working on ./Run.mb diffing standard.tmp with toverify.tmp PASSED ============================================================== cd pbsa_aug_c2 && ./Run.ion.min diffing save/Cl.out.save with Cl.out PASSED ============================================================== diffing save/MG.out.save with MG.out PASSED ============================================================== cd pbsa_memb_test && ./Run.memb.test initializing variables begining testing for aquaporin_coil parsing option set building input file Running Calculations for aquaporin_coil.mem.4.0.out diffing save/aquaporin_coil.mem.4.0.out.save with aquaporin_coil.mem.4.0.out PASSED ============================================================== building input file Running Calculations for aquaporin_coil.mem.16.0.out diffing save/aquaporin_coil.mem.16.0.out.save with aquaporin_coil.mem.16.0.out PASSED ============================================================== building input file Running Calculations for aquaporin_coil.mem.64.0.out diffing save/aquaporin_coil.mem.64.0.out.save with aquaporin_coil.mem.64.0.out PASSED ============================================================== cd pbsa_memb_test && ./Run.solv.test initializing variables begining testing for aquaporin_coil parsing option set building input file Running Calculations for aquaporin_coil.vac.out diffing save/aquaporin_coil.vac.out.save with aquaporin_coil.vac.out PASSED ============================================================== parsing option set building input file Running Calculations for aquaporin_coil.wat.out diffing save/aquaporin_coil.wat.out.save with aquaporin_coil.wat.out PASSED ============================================================== parsing option set building input file Running Calculations for aquaporin_coil.mem.out diffing save/aquaporin_coil.mem.out.save with aquaporin_coil.mem.out PASSED ============================================================== cd pbsa_phiout && ./Run.dmp.min diffing mdout.dmp.phi1.min.save with mdout.dmp.phi1.min PASSED ============================================================== diffing mdout.dmp.phi2.min.save with mdout.dmp.phi2.min PASSED ============================================================== diffing pbsa_phi.dx.save with pbsa_phi.dx PASSED ============================================================== diffing pbsa_phi.phi.save with pbsa_phi.phi PASSED ============================================================== cd gbnsr6 && ./Run.gbnsr6.min diffing undecan_2_one.alpb.out.save with undecan_2_one.alpb.out PASSED ============================================================== diffing undecan_2_one.radii.out.save with undecan_2_one.radii.out PASSED ============================================================== diffing undecan_2_one.chagb.out.save with undecan_2_one.chagb.out PASSED ============================================================== cd mmpbsa_py && make test make[3]: Entering directory `/home/anwesha/amber14/AmberTools/test/mmpbsa_py' cd 07_Comprehensive && ./Run.comprehensive ./Run.comprehensive: Program error make[3]: *** [COMPREHENSIVE] Error 1 make[3]: Target `test' not remade because of errors. make[3]: Leaving directory `/home/anwesha/amber14/AmberTools/test/mmpbsa_py' make[2]: *** [test.mmpbsa] Error 2 cd parmed/normag_prmtop &t' not remade because of errors. ./Run.parmed ./Run.parmed: Program error make[2]: *** [test.parmed] Error 1 cd elsize && ./Run.elsize diffing elsize_out.trxox.save with elsize_out.trxox PASSED ============================================================== cd ./sqm/c2h2 && ./Run diffing c2h2.pm3.sp.out.save with c2h2.pm3.sp.out PASSED ============================================================== diffing c2h2.pm6.sp.out.save with c2h2.pm6.sp.out PASSED ============================================================== diffing c2h2.pm3.go.out.save with c2h2.pm3.go.out PASSED ============================================================== diffing c2h2.pm6.go.out.save with c2h2.pm6.go.out PASSED ============================================================== cd ./sqm/ch3f && ./Run diffing ch3f.pm3.sp.out.save with ch3f.pm3.sp.out PASSED ============================================================== diffing ch3f.pm6.sp.out.save with ch3f.pm6.sp.out PASSED ============================================================== diffing ch3f.pm3.go.out.save with ch3f.pm3.go.out PASSED ============================================================== diffing ch3f.pm6.go.out.save with ch3f.pm6.go.out PASSED ============================================================== cd ./sqm/nma && ./Run DFTB SLKO files not found - Skipping DFTB tests... diffing nma.pm3.sp.out.save with nma.pm3.sp.out PASSED ============================================================== diffing nma.pm6.sp.out.save with nma.pm6.sp.out PASSED ============================================================== diffing nma.pm3.go.out.save with nma.pm3.go.out PASSED ============================================================== diffing nma.pm6.go.out.save with nma.pm6.go.out PASSED ============================================================== cd ./sqm/znh+ && ./Run diffing znh+.pm3.sp.out.save with znh+.pm3.sp.out PASSED ============================================================== diffing znh+.znb.sp.out.save with znh+.znb.sp.out PASSED ============================================================== diffing znh+.pm3.go.out.save with znh+.pm3.go.out PASSED ============================================================== diffing znh+.znb.go.out.save with znh+.znb.go.out PASSED ============================================================== cd ./sqm/h2s && ./Run DFTB SLKO files not found - Skipping DFTB tests... diffing h2s.mndod.sp.out.save with h2s.mndod.sp.out PASSED ============================================================== diffing h2s.pm6.sp.out.save with h2s.pm6.sp.out PASSED ============================================================== diffing h2s.mndod.go.out.save with h2s.mndod.go.out PASSED ============================================================== cd ./sqm/dhplus && ./Run diffing meoh_nh3.pm6-dh+.sp.out.save with meoh_nh3.pm6-dh+.sp.out PASSED ============================================================== diffing meoh_nh3.pm6-dh+.go.out.save with meoh_nh3.pm6-dh+.go.out PASSED ============================================================== cd ./sqm/fecp2 && ./Run diffing fecp2.pm6.sp.out.save with fecp2.pm6.sp.out PASSED ============================================================== cd ./sqm/external_charges && ./Run DFTB SLKO files not found - Skipping DFTB tests... diffing qm_adenine.pm3.sp.out.save with qm_adenine.pm3.sp.out PASSED ============================================================== diffing qm_thymine.pm3.sp.out.save with qm_thymine.pm3.sp.out PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/spc-kh && ./Run.spc; fi diffing spc.xvv.delhv0.save with spc.xvv.delhv0 PASSED ============================================================== diffing spc.xvv.delhv0_dT.save with spc.xvv.delhv0_dT PASSED ============================================================== diffing spc.xvv.xvv.save with spc.xvv.xvv PASSED ============================================================== diffing spc.xvv.xvv_dT.save with spc.xvv.xvv_dT PASSED ============================================================== diffing spc.xvv.other.save with spc.xvv.other PASSED ============================================================== diffing spc.uvv.save with spc.uvv PASSED ============================================================== diffing spc.gvv.save with spc.gvv PASSED ============================================================== diffing spc.cvv.save with spc.cvv PASSED ============================================================== diffing spc.cvv_dT.save with spc.cvv_dT PASSED ============================================================== diffing spc.therm.save with spc.therm PASSED ============================================================== diffing spc.exnvv.save with spc.exnvv PASSED ============================================================== diffing spc.nvv.save with spc.nvv PASSED ============================================================== diffing spc.n00.save with spc.n00 PASSED ============================================================== diffing spc.q00.save with spc.q00 PASSED ============================================================== diffing spc.hvv.save with spc.hvv PASSED ============================================================== diffing spc.hvv_dT.save with spc.hvv_dT PASSED ============================================================== diffing spc.svv.save with spc.svv PASSED ============================================================== diffing spc.bvv.save with spc.bvv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/spc-psen && ./Run.spc-nacl-3; fi diffing spc-nacl-3.xvv.delhv0.save with spc-nacl-3.xvv.delhv0 PASSED ============================================================== diffing spc-nacl-3.xvv.delhv0_dT.save with spc-nacl-3.xvv.delhv0_dT PASSED ============================================================== diffing spc-nacl-3.xvv.xvv.save with spc-nacl-3.xvv.xvv PASSED ============================================================== diffing spc-nacl-3.xvv.xvv_dT.save with spc-nacl-3.xvv.xvv_dT PASSED ============================================================== diffing spc-nacl-3.xvv.other.save with spc-nacl-3.xvv.other PASSED ============================================================== diffing spc-nacl-3.uvv.save with spc-nacl-3.uvv PASSED ============================================================== diffing spc-nacl-3.gvv.save with spc-nacl-3.gvv PASSED ============================================================== diffing spc-nacl-3.gvv_dT.save with spc-nacl-3.gvv_dT PASSED ============================================================== diffing spc-nacl-3.cvv.save with spc-nacl-3.cvv PASSED ============================================================== diffing spc-nacl-3.cvv_dT.save with spc-nacl-3.cvv_dT PASSED ============================================================== diffing spc-nacl-3.therm.save with spc-nacl-3.therm PASSED ============================================================== diffing spc-nacl-3.exnvv.save with spc-nacl-3.exnvv PASSED ============================================================== diffing spc-nacl-3.nvv.save with spc-nacl-3.nvv PASSED ============================================================== diffing spc-nacl-3.n00.save with spc-nacl-3.n00 PASSED ============================================================== diffing spc-nacl-3.q00.save with spc-nacl-3.q00 PASSED ============================================================== diffing spc-nacl-3.hvv.save with spc-nacl-3.hvv PASSED ============================================================== diffing spc-nacl-3.hvv_dT.save with spc-nacl-3.hvv_dT PASSED ============================================================== diffing spc-nacl-3.svv.save with spc-nacl-3.svv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/spc-hnc && ./Run.spc-lj; fi diffing spc-lj.xvv.delhv0.save with spc-lj.xvv.delhv0 PASSED ============================================================== diffing spc-lj.xvv.delhv0_dT.save with spc-lj.xvv.delhv0_dT PASSED ============================================================== diffing spc-lj.xvv.xvv.save with spc-lj.xvv.xvv PASSED ============================================================== diffing spc-lj.xvv.xvv_dT.save with spc-lj.xvv.xvv_dT PASSED ============================================================== diffing spc-lj.xvv.other.save with spc-lj.xvv.other PASSED ============================================================== diffing spc-lj.uvv.save with spc-lj.uvv PASSED ============================================================== diffing spc-lj.gvv.save with spc-lj.gvv PASSED ============================================================== diffing spc-lj.cvv.save with spc-lj.cvv PASSED ============================================================== diffing spc-lj.therm.save with spc-lj.therm PASSED ============================================================== diffing spc-lj.exnvv.save with spc-lj.exnvv PASSED ============================================================== diffing spc-lj.nvv.save with spc-lj.nvv PASSED ============================================================== diffing spc-lj.n00.save with spc-lj.n00 PASSED ============================================================== diffing spc-lj.q00.save with spc-lj.q00 PASSED ============================================================== diffing spc-lj.hvv.save with spc-lj.hvv PASSED ============================================================== diffing spc-lj.svv.save with spc-lj.svv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/spc-mv0 && ./Run.spc; fi diffing spc.xvv.delhv0.save with spc.xvv.delhv0 PASSED ============================================================== diffing spc.xvv.delhv0_dT.save with spc.xvv.delhv0_dT PASSED ============================================================== diffing spc.xvv.xvv.save with spc.xvv.xvv PASSED ============================================================== diffing spc.xvv.xvv_dT.save with spc.xvv.xvv_dT PASSED ============================================================== diffing spc.xvv.other.save with spc.xvv.other PASSED ============================================================== diffing spc.uvv.save with spc.uvv PASSED ============================================================== diffing spc.gvv.save with spc.gvv PASSED ============================================================== diffing spc.cvv.save with spc.cvv PASSED ============================================================== diffing spc.therm.save with spc.therm PASSED ============================================================== diffing spc.exnvv.save with spc.exnvv PASSED ============================================================== diffing spc.nvv.save with spc.nvv PASSED ============================================================== diffing spc.n00.save with spc.n00 PASSED ============================================================== diffing spc.q00.save with spc.q00 PASSED ============================================================== diffing spc.hvv.save with spc.hvv PASSED ============================================================== diffing spc.svv.save with spc.svv PASSED ============================================================== diffing spc.bvv.save with spc.bvv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/lj-py && ./Run.lj; fi diffing lj.xvv.delhv0.save with lj.xvv.delhv0 PASSED ============================================================== diffing lj.xvv.delhv0_dT.save with lj.xvv.delhv0_dT PASSED ============================================================== diffing lj.xvv.xvv.save with lj.xvv.xvv PASSED ============================================================== diffing lj.xvv.xvv_dT.save with lj.xvv.xvv_dT PASSED ============================================================== diffing lj.xvv.other.save with lj.xvv.other PASSED ============================================================== diffing lj.uvv.save with lj.uvv PASSED ============================================================== diffing lj.gvv.save with lj.gvv PASSED ============================================================== diffing lj.cvv.save with lj.cvv PASSED ============================================================== diffing lj.therm.save with lj.therm PASSED ============================================================== diffing lj.exnvv.save with lj.exnvv PASSED ============================================================== diffing lj.nvv.save with lj.nvv PASSED ============================================================== diffing lj.n00.save with lj.n00 PASSED ============================================================== diffing lj.hvv.save with lj.hvv PASSED ============================================================== diffing lj.svv.save with lj.svv PASSED ============================================================== diffing lj.bvv.save with lj.bvv PASSED ============================================================== if [ -n "testrism" ]; then cd ./rism1d/tip3p-kh && ./Run.tip3p; fi diffing tip3p.xvv.delhv0.save with tip3p.xvv.delhv0 PASSED ============================================================== diffing tip3p.xvv.delhv0_dT.save with tip3p.xvv.delhv0_dT PASSED ============================================================== diffing tip3p.xvv.xvv.save with tip3p.xvv.xvv PASSED ============================================================== diffing tip3p.xvv.xvv_dT.save with tip3p.xvv.xvv_dT PASSED ============================================================== diffing tip3p.xvv.other.save with tip3p.xvv.other PASSED ============================================================== diffing tip3p.uvv.save with tip3p.uvv PASSED ============================================================== diffing tip3p.gvv.save with tip3p.gvv PASSED ============================================================== diffing tip3p.cvv.save with tip3p.cvv PASSED ============================================================== diffing tip3p.therm.save with tip3p.therm PASSED ============================================================== diffing tip3p.exnvv.save with tip3p.exnvv PASSED ============================================================== diffing tip3p.nvv.save with tip3p.nvv PASSED ============================================================== diffing tip3p.n00.save with tip3p.n00 PASSED ============================================================== diffing tip3p.q00.save with tip3p.q00 PASSED ============================================================== diffing tip3p.hvv.save with tip3p.hvv PASSED ============================================================== diffing tip3p.svv.save with tip3p.svv PASSED ============================================================== cd amberlite && ./Run.pdb4amber diffing 3ptb_amber_dpy.pdb.save with 3ptb_amber_dpy.pdb PASSED ============================================================== diffing 3ptb_amber.pdb.save with 3ptb_amber.pdb PASSED ============================================================== diffing 3ptb_amber_ph.pdb.save with 3ptb_amber_ph.pdb PASSED ============================================================== diffing 3ptb_amber_H.pdb.save with 3ptb_amber_H.pdb PASSED ============================================================== diffing 3ptb_amber_Hnoter.pdb.save with 3ptb_amber_Hnoter.pdb PASSED ============================================================== diffing 3ptb_amber_pipe.pdb.save with 3ptb_amber_pipe.pdb PASSED ============================================================== diffing 4lzt_amber_mostpop.pdb.save with 4lzt_amber_mostpop.pdb PASSED ============================================================== diffing 4lzt_amber.pdb.save with 4lzt_amber.pdb PASSED ============================================================== diffing HIStest_amber.pdb.save with HIStest_amber.pdb PASSED ============================================================== diffing 3ptb_amber_reduce.pdb.save with 3ptb_amber_reduce.pdb PASSED ============================================================== diffing 3ptb_amber_reduce.pdb.save with 3ptb_amber_reduce_stdin.pdb PASSED ============================================================== diffing 2mpi_amber_model.pdb.save with 2mpi_amber_model.pdb PASSED ============================================================== cd paramfit && make -k test make[3]: Entering directory `/home/anwesha/amber14/AmberTools/test/paramfit' cd write_qminput_nma; ./run_test.x *** Create Gaussian Input Files (new prmtop) *** diffing saved_output/Job.0.gjf.saved with Job.0.gjf PASSED ============================================================== diffing saved_output/Job.1.gjf.saved with Job.1.gjf PASSED ============================================================== diffing saved_output/Job.2.gjf.saved with Job.2.gjf PASSED ============================================================== diffing saved_output/Job.3.gjf.saved with Job.3.gjf PASSED ============================================================== diffing saved_output/Job.4.gjf.saved with Job.4.gjf PASSED ============================================================== cd simplex_perfect_fit_NMA; ./run_test.x *** NMA Simplex Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== cd ga_perfect_fit_NMA; ./run_test.x *** NMA Genetic Algorithm Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== diffing saved_output/frcmod.saved with frcmod PASSED ============================================================== cd dihedral_least_squares_NMA; ./run_test.x *** NMA Dihedral Linear Algorithm Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== diffing saved_output/frcmod.saved with frcmod PASSED ============================================================== make[3]: Leaving directory `/home/anwesha/amber14/AmberTools/test/paramfit' cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.test CLEANING CALCULATING TEST: 01_GenerateSnapshots CHECKING IN TEST: 01_GenerateSnapshots diffing /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/01_GenerateSnapshots/test_com.crd.4.save with /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/01_GenerateSnapshots/test_com.crd.4 PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/01_GenerateSnapshots/test_lig.crd.4.save with /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/01_GenerateSnapshots/test_lig.crd.4 PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/01_GenerateSnapshots/test_rec.crd.4.save with /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/01_GenerateSnapshots/test_rec.crd.4 PASSED ============================================================== CALCULATING TEST: 02_MMPBSA_Stability CHECKING IN TEST: 02_MMPBSA_Stability diffing /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/02_MMPBSA_Stability/test_statistics.out.save with /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/02_MMPBSA_Stability/test_statistics.out PASSED ============================================================== CALCULATING TEST: 03_MMPBSA_Binding CHECKING IN TEST: 03_MMPBSA_Binding diffing /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/03_MMPBSA_Binding/test_statistics.out.save with /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/03_MMPBSA_Binding/test_statistics.out PASSED ============================================================== CALCULATING TEST: 05_MMPBSA_Decomp_Residue CHECKING IN TEST: 05_MMPBSA_Decomp_Residue diffing /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/test_statistics.out.save with /home/anwesha/amber14/AmberTools/src/mm_pbsa/Examples/05_MMPBSA_Decomp_Residue/test_statistics.out PASSED ============================================================== cd ../src/FEW/examples/test && ./Run.few.test ######################################################################### PERFORMING FEW TESTS In case all of the tests below fail likely the system specific path to the locally installed Perl libraries was not found. Please consult the file /home/anwesha/amber14/AmberTools/src/FEW/examples/test/few.log for more details about the cause for the program error and on how to solve it. CLEANING PERFORMING TEST 01: Step1 of RESP charge calculation CHECKING IN TEST 01: Step1 of RESP charge calculation diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/gauss_setup/L51a/L51a.gcrt with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/gauss/L51a/L51a.gcrt PASSED ============================================================== PERFORMING TEST 02: Step2 of RESP charge calculation and setup of MD simulations CHECKING IN TEST 02: Step2 of RESP charge calculation and setup of MD simulations diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/gauss_setup/L51a/L51a.gout.xyz with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/gauss/L51a/L51a.gout.xyz PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_resp.lib with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/L51a/L51a_resp.lib PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a.frcmod with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/L51a/L51a.frcmod PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_com.pdb with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/L51a/L51a_com.pdb PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_rec.pdb with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/L51a/L51a_rec.pdb PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap/L51a/L51a_lig.pdb with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/L51a/L51a_lig.pdb PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/cryst/L51a_solv_com.crd with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_com.crd PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/cryst/L51a_solv_rec.crd with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_rec.crd PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/cryst/L51a_solv_lig.crd with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_resp/L51a/cryst/L51a_solv_lig.crd PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/lig/equi/md_nvt_red_06.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_resp/L51a/lig/equi/md_nvt_red_06.in PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/rec/equi/md_nvt_red_06.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_resp/rec/equi/md_nvt_red_06.in PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/L51a/lig/prod/md_prod_001.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_resp/L51a/lig/prod/md_prod_001.in PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_resp_setup/rec/prod/md_prod_001.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_resp/rec/prod/md_prod_001.in PASSED ============================================================== PERFORMING TEST 03: Setup of MMPBSA calculations according to 1-trajectory approach CHECKING IN TEST 03: Setup of MMPBSA calculations according to 1-trajectory approach diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/calc_r_1t/L51a/snapshots/L51a_lig.crd.5 with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/calc_r_1t/L51a/snapshots/L51a_lig.crd.5 PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/calc_r_1t/L51a/topo/L51a_gb0_pb3_lig.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/calc_r_1t/L51a/topo/L51a_gb0_pb3_lig.top PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/calc_r_1t/L51a/s2_4_1/pb3_gb0/mmpbsa.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/calc_r_1t/L51a/s2_4_1/pb3_gb0/mmpbsa.in PASSED ============================================================== PERFORMING TEST 04: Setup of LIE analysis CHECKING IN TEST 04: Setup of LIE analysis diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/topo/lig.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/topo/lig.top PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/topo/tot.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/topo/tot.top PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/topo/wat.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/topo/wat.top PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/s_lig/md_prod_001_nobox.mdcrd with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/s_lig/md_prod_001_nobox.mdcrd PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/s_tot/md_prod_001_nobox.mdcrd with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/s_tot/md_prod_001_nobox.mdcrd PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/lie_resp/L51a/lig/s_wat/md_prod_001_nobox.mdcrd with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/lie_resp/L51a/lig/s_wat/md_prod_001_nobox.mdcrd PASSED ============================================================== PERFORMING TEST 05: TI step1, Preparation of coordinate and topology files CHECKING IN TEST 05: TI step1, Preparation of coordinate and toplogy files diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/match_list.txt with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/match_list.txt PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/setup/L51a_lig_TIin.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/setup/L51a_lig_TIin.top PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/setup/L51b_lig_TIin.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/setup/L51b_lig_TIin.top PASSED ============================================================== PERFORMING TEST 06: TI step2A, Preparation of files for TI equilibration CHECKING IN TEST 06: TI step2A, Preparation of files for TI equilibration diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/group_equi01_l2 with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/group_equi01_l2 PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/LFa_equi01_v0_l2.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/LFa_equi01_v0_l2.in PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/group_prod01_l2 with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/group_prod01_l2 PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/LFa_prod01_v0_l2.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/LFa_prod01_v0_l2.in PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/equi/lig/LFa_lig_TIin.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/equi/lig/LFa_lig_TIin.top PASSED ============================================================== PERFORMING TEST 07: TI step3, Preparation of files for TI production CHECKING IN TEST 07: TI step3, Preparation of files for TI production diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/TI_resp_setup/L51a_L51b/TI_results/TI_dG.out with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/TI_resp/L51a_L51b/TI_results/TI_dG.out PASSED ============================================================== PERFORMING TEST 08: Setup of MD simulations with explicit membrane and AM1 charges CHECKING IN TEST 08: Setup of MD simulations with explicit membrane and AM1 charges diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_am1.lib with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/AMT/AMT_am1.lib PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_com.pdb with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/AMT/AMT_com.pdb PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_rec.pdb with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/AMT/AMT_rec.pdb PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/leap_setup_membrane/AMT/AMT_lig.pdb with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/leap/AMT/AMT_lig.pdb PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_am1_setup_membrane/AMT/cryst/AMT_solv_com.crd with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_am1/AMT/cryst/AMT_solv_com.crd PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_am1_setup_membrane/AMT/com/equi/md3npt.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_am1/AMT/com/equi/md3npt.in PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/MD_am1_setup_membrane/AMT/com/prod/md_prod_001.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/MD_am1/AMT/com/prod/md_prod_001.in PASSED ============================================================== PERFORMING TEST 09: Setup of MMPBSA calculations with implicit membrane CHECKING IN TEST 09: Setup of MMPBSA calculations with implicit membrane diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/snapshots/AMT_com.crd.3 with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/snapshots/AMT_com.crd.3 PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/topo/AMT_gb0_pb3_com.top with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/topo/AMT_gb0_pb3_com.top PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/s1_3_1/pb3_gb0/mmpbsa.in with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/s1_3_1/pb3_gb0/mmpbsa.in PASSED ============================================================== diffing /home/anwesha/amber14/AmberTools/src/FEW/examples/test/saved/calc_a_1t_ImplMem/AMT/pqr_snaps/AMT_rec.pqr.3 with /home/anwesha/amber14/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/pqr_snaps/AMT_rec.pqr.3 PASSED ============================================================== cd cphstats && ./Run.cphstats diffing md2_cpout.pH_2.00.save with md2_cpout.pH_2.00 PASSED ============================================================== diffing md3_cpout.pH_4.50.save with md3_cpout.pH_4.50 PASSED ============================================================== diffing pH_2.00.calcpka.save with pH_2.00.calcpka PASSED ============================================================== diffing pH_2.50.calcpka.save with pH_2.50.calcpka PASSED ============================================================== diffing pH_3.00.calcpka.save with pH_3.00.calcpka PASSED ============================================================== diffing pH_3.50.calcpka.save with pH_3.50.calcpka PASSED ============================================================== diffing pH_4.00.calcpka.save with pH_4.00.calcpka PASSED ============================================================== diffing pH_4.50.calcpka.save with pH_4.50.calcpka PASSED ============================================================== diffing pH_5.00.calcpka.save with pH_5.00.calcpka PASSED ============================================================== diffing pH_5.50.calcpka.save with pH_5.50.calcpka PASSED ============================================================== diffing pH_6.00.calcpka.save with pH_6.00.calcpka PASSED ============================================================== diffing pH_6.50.calcpka.save with pH_6.50.calcpka PASSED ============================================================== diffing pH_7.00.calcpka.save with pH_7.00.calcpka PASSED ============================================================== diffing pH_7.50.calcpka.save with pH_7.50.calcpka PASSED ============================================================== diffing pH_2.00.calcpka.save with pH_2.00.calcpka PASSED ============================================================== diffing cphstats_output.txt.save with cphstats_output.txt PASSED ============================================================== diffing running_avgs.dat.save with running_avgs.dat PASSED ============================================================== diffing running_avg.dat.save with running_avg.dat PASSED ============================================================== diffing running_pKa.dat.save with running_pKa.dat PASSED ============================================================== diffing chunk.dat.save with chunk.dat PASSED ============================================================== diffing chunk_deprot.dat.save with chunk_deprot.dat PASSED ============================================================== diffing chunk_pka.dat.save with chunk_pka.dat PASSED ============================================================== diffing cumulative.dat.save with cumulative.dat PASSED ============================================================== diffing cumulative_deprot.dat.save with cumulative_deprot.dat PASSED ============================================================== diffing cumulative_pka.dat.save with cumulative_pka.dat PASSED ============================================================== diffing pop.dat.save with pop.dat PASSED ============================================================== diffing conditional.dat.save with conditional.dat PASSED ============================================================== diffing conditional_chunks.dat.save with conditional_chunks.dat PASSED ============================================================== cd charmmlipid2amber && ./Run.charmmlipid2amber diffing charmmlipid2amber.out.save with charmmlipid2amber.out PASSED ============================================================== cd cpinutil && ./Run.cpin diffing cpin1.save with cpin1 possible FAILURE: check cpin1.dif ============================================================== diffing cpin2.save with cpin2 possible FAILURE: check cpin2.dif ============================================================== diffing cpin3.save with cpin3 possible FAILURE: check cpin3.dif ============================================================== diffing cpin3.save with cpin3.1 possible FAILURE: check cpin3.1.dif ============================================================== diffing cpin4.save with cpin4 possible FAILURE: check cpin4.dif ============================================================== diffing cpin5.save with cpin5 possible FAILURE: check cpin5.dif ============================================================== diffing cpin6.save with cpin6 possible FAILURE: check cpin6.dif ============================================================== diffing cpin7.save with cpin7 possible FAILURE: check cpin7.dif ============================================================== make[2]: Target `test.serial' not remade because of errors. make[2]: Leaving directory `/home/anwesha/amber14/AmberTools/test' make[2]: Entering directory `/home/anwesha/amber14/test' cd dmp && ./Run.dmp diffing mdout.dmp.save with mdout.dmp PASSED ============================================================== cd adenine && ./Run.adenine diffing mdout.adenine.save with mdout.adenine PASSED ============================================================== cd variable_14 && ./Run.variable_14_igb1 diffing variable_14_igb1.mdout.save with variable_14_igb1.mdout PASSED ============================================================== cd cytosine && ./Run.cytosine diffing cytosine.out.save with cytosine.out PASSED ============================================================== cd nonper && ./Run.nonper diffing mdout.nonper.save with mdout.nonper PASSED ============================================================== cd nonper && ./Run.nonper.belly diffing mdout.belly.save with mdout.belly PASSED ============================================================== cd nonper && ./Run.nonper.belly.mask diffing mdout.belly.mask.save with mdout.belly.mask PASSED ============================================================== cd nonper && ./Run.nonper.min diffing mdout.min.save with mdout.min PASSED ============================================================== cd nonper && ./Run.cap diffing mdout.cap.save with mdout.cap PASSED ============================================================== cd nonper && ./Run.nonper.nocut diffing mdout.nocut.save with mdout.nocut PASSED ============================================================== cd tip4p && ./Run.tip4p diffing mdout.tip4p.save with mdout.tip4p PASSED ============================================================== cd tip4p && ./Run.tip4p_mcbar diffing mdout.mcbar.tip4p.sander.save with mdout.mcbar.tip4p PASSED ============================================================== diffing mdout.mcbar_aniso.tip4p.sander.save with mdout.mcbar_aniso.tip4p PASSED ============================================================== cd tip4p && ./Run.tip4p_nve diffing mdout.tip4p_nve.save with mdout.tip4p_nve PASSED ============================================================== cd tip5p && ./Run.tip5p diffing mdout.tip5p.save with mdout.tip5p PASSED ============================================================== cd tip5p && ./Run.tip5p_nve diffing mdout.tip5p_nve.save with mdout.tip5p_nve PASSED ============================================================== cd 4096wat && ./Run.pure_wat diffing mdout.pure_wat.save with mdout.pure_wat PASSED ============================================================== cd 4096wat && ./Run.pure_wat_nmr_temp_reg diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp PASSED ============================================================== cd 4096wat && ./Run.vrand diffing mdout.vrand.save with mdout.vrand PASSED ============================================================== cd 4096wat && ./Run.frcdmp diffing mdout.pure_wat2.save with mdout.pure_wat2 PASSED ============================================================== diffing mdfrc_cmp.save with mdfrc_cmp PASSED ============================================================== cd 4096wat_oct && ./Run.pure_wat_oct diffing mdout.pure_wat_oct.save with mdout.pure_wat_oct PASSED ============================================================== diffing mdcrd.pure_wat_oct.save with mdcrd.pure_wat_oct PASSED ============================================================== cd dhfr && ./Run.dhfr && ./Run.dhfr prmtop_an diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== diffing mdout.dhfr.save with mdout.dhfr PASSED ============================================================== cd dhfr && ./Run.dhfr.noboxinfo diffing mdout.dhfr.noboxinfo.save with mdout.dhfr.noboxinfo PASSED ============================================================== cd dhfr && ./Run.dhfr.noshake diffing mdout.dhfr.noshake.save with mdout.dhfr.noshake PASSED ============================================================== cd dhfr && ./Run.dhfr.min diffing mdout.dhfr.min.save with mdout.dhfr.min PASSED ============================================================== cd dhfr && ./Run.dhfr.min_prcg diffing mdout.dhfr.min_prcg.save with mdout.dhfr.min_prcg PASSED ============================================================== cd dhfr && ./Run.dhfr.lmodxmin diffing mdout.dhfr.lmodxmin.save with mdout.dhfr.lmodxmin PASSED ============================================================== cd ff14ipq && ./Run.ff14ipq diffing mdout.ff14ipq.save with mdout.ff14ipq PASSED ============================================================== cd variable_14 && ./Run.variable_14_ntb1 diffing variable_14_ntb1.mdout.save with variable_14_ntb1.mdout PASSED ============================================================== cd gact_ips && ./Run.ips diffing mdout.ips.save with mdout.ips PASSED ============================================================== cd gact_ips && ./Run.ipsnve diffing mdout.ipsnve.save with mdout.ipsnve PASSED ============================================================== cd gact_ips && ./Run.ips_dfft diffing mdout.ips_dfft.save with mdout.ips_dfft PASSED ============================================================== cd gact_ips && ./Run.ips_vacuum diffing mdout.ips_vacuum.save with mdout.ips_vacuum PASSED ============================================================== cd polarizable_water && ./Run.pol_wat diffing mdout.polwat.save with mdout.polwat PASSED ============================================================== cd ubiquitin && ./Run.ubiquitin diffing mdout.ubiquitin.save with mdout.ubiquitin PASSED ============================================================== diffing mden.save with mden PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== cd dna_pol && ./Run.dna_pol diffing mdout.dna_pol.save with mdout.dna_pol PASSED ============================================================== cd trx && ./Run.trx diffing mdout.trx.save with mdout.trx PASSED ============================================================== cd trx && ./Run.trx.cpln diffing mdout.trx.cpln.save with mdout.trx.cpln PASSED ============================================================== cd rdc && ./Run.dip diffing gcg.dip.o.save with gcg.dip.o PASSED ============================================================== cd rdc && ./Run.csa diffing gcg.csa.o.save with gcg.csa.o PASSED ============================================================== cd rdc && ./Run.csa_min diffing gcg.csa_min.o.save with gcg.csa_min.o PASSED ============================================================== cd pcsa && ./Run.dip diffing stem.dip.o.save with stem.dip.o PASSED ============================================================== cd pcsa && ./Run.csa diffing stem.csa.o.save with stem.csa.o PASSED ============================================================== cd pcsa && ./Run.csa2 diffing stem.csa2.o.save with stem.csa2.o PASSED ============================================================== cd pcsa && ./Run.csa_min diffing stem.csa_min.o.save with stem.csa_min.o PASSED ============================================================== cd tgtmd/change_target && ./Run.tgtmd SANDER: Targeted MD with changing target diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.rms && ./Run.tgtmd SANDER: Targeted MD with changing target and fit/rmsd to different regions diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/change_target.ntr && ./Run.tgtmd SANDER: Targeted MD with changing target and restraints diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/conserve_ene && ./Run.tgtmd SANDER: Targeted MD energy conservation test diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd tgtmd/minimize && ./Run.tgtmin SANDER: Targeted minimization diffing tgtmin.out.save with tgtmin.out PASSED ============================================================== cd tgtmd/PME && ./Run.tgtPME SANDER: Targeted MD with PME diffing tgtmd.out.save with tgtmd.out PASSED ============================================================== cd mtmdtest && ./Run.mtmdtest SANDER: Multiply-targeted MD, new to AMBER 11 Tested on an RNA duplex. diffing mtmdtest.out.save with mtmdtest.out PASSED ============================================================== diffing mtmdtest.mdcrd.save with mtmdtest.mdcrd PASSED ============================================================== cd trajene && ./Run.trajene diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.save with mdcrd.out PASSED ============================================================== cd trajene_box && ./Run.trajene diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.save with mdcrd.out PASSED ============================================================== cd trajene_netcdf && ./Run.trajene /home/anwesha/amber14/include/netcdf.mod diffing trajene.out.save with trajene.out PASSED ============================================================== diffing mdcrd.out.nc.save with mdcrd.out.nc PASSED ============================================================== cd alp && ./Run.alp diffing mdout.alp.save with mdout.alp PASSED ============================================================== cd umbrella && ./Run.umbrella diffing mdout.umbrella.save with mdout.umbrella PASSED ============================================================== diffing chi_vs_t.save with chi_vs_t PASSED ============================================================== cd noesy && ./Run.noesy diffing noesy.out.save with noesy.out PASSED ============================================================== cd jar && ./Run.jarz diffing mdout.jar.save with mdout.jar PASSED ============================================================== diffing dist_vs_t.save with dist_vs_t PASSED ============================================================== cd plane_plane_restraint && ./Run.dinuc_plpt SANDER: Dinucleoside restrained with new plane-point angle restraint that was defined with new natural language restraint input. diffing mdout.dinucAU_plpt.save with mdout.dinucAU_plpt PASSED ============================================================== diffing dinuc_plpt_vs_t.save with dinuc_plpt_vs_t PASSED ============================================================== cd plane_plane_restraint && ./Run.dinuc_pln SANDER: Dinucleoside restrained with new plane-plane angle restraint that was defined with new natural language restraint input. diffing mdout.dinucAU_pln.save with mdout.dinucAU_pln PASSED ============================================================== diffing dinuc_pln_vs_t.save with dinuc_pln_vs_t PASSED ============================================================== cd iwrap2 && ./Run.iwrap2 diffing mdout.iw2.save with mdout.iw2 PASSED ============================================================== diffing mdcrd.iw2.save with mdcrd.iw2 PASSED ============================================================== diffing rstrt.iw2.save with rstrt.iw2 PASSED ============================================================== cd idecomp1 && ./run_idecomp1.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd idecomp4 && ./run_idecomp4.sh diffing decomp.out.save with decomp.out PASSED ============================================================== cd bintraj && ./Run.bintraj /home/anwesha/amber14/include/netcdf.mod diffing nc_headers.save with nc_headers PASSED ============================================================== cd netcdf && make -k test OPT=/home/anwesha/amber14/include/netcdf.mod make[3]: Entering directory `/home/anwesha/amber14/test/netcdf' Netcdf MD Restart Write Test diffing textmd.rst7.save with textmd.rst7 PASSED ============================================================== Netcdf Minimization Restart Write Test diffing textmin.rst7.save with textmin.rst7 PASSED ============================================================== Restrained MD with netcdf Restart Reference Coords Test diffing md.rst7.save with md.rst7 PASSED ============================================================== diffing ene.dat.save with ene.dat PASSED ============================================================== Netcdf MD restart read test, ntx=5 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== Netcdf MD restart read test, ntx=1 diffing md1.rst7 with md2.rst7 PASSED ============================================================== diffing ene1 with ene2 PASSED ============================================================== diffing md.crd.save with md.crd PASSED ============================================================== make[3]: Leaving directory `/home/anwesha/amber14/test/netcdf' cd csurften && ./Run.csurften_z-dir diffing mdout.csurften_z-dir.save with mdout.csurften_z-dir PASSED ============================================================== cd csurften && ./Run.csurften_z-dir_npt_3 diffing mdout.csurften_z-dir_npt_3.save with mdout.csurften_z-dir_npt_3 PASSED ============================================================== cd linear_interaction_energy && ./Run.lie diffing mdout.lie.save with mdout.lie PASSED ============================================================== cd nmropt && make all make[3]: Entering directory `/home/anwesha/amber14/test/nmropt' cd gb/angle && ./Run.nmropt_1angle_gb diffing mdout.save with mdout PASSED ============================================================== diffing angle_gb_vs_t.save with angle_gb_vs_t PASSED ============================================================== cd gb/distance && ./Run.dist_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/distance_COM && ./Run.distCOM_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_distance && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing dist_gb_vs_t.save with dist_gb_vs_t PASSED ============================================================== cd gb/jar_distance_COM && ./Run.jar_gb diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_gb_vs_t.save with distCOM_gb_vs_t PASSED ============================================================== cd gb/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_gb.dat.save with jartorsion_gb.dat PASSED ============================================================== cd gb/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_gb.dat.save with torsion_gb.dat PASSED ============================================================== cd gb/tautp && ./Run.nmropt_1tautp_gb diffing mdout.save with mdout PASSED ============================================================== cd gb/temp && ./Run.nmropt_1temp_gb diffing mdout.save with mdout PASSED ============================================================== cd pme/angle && ./Run.nmropt_1angle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing angle_pbc_vs_t.save with angle_pbc_vs_t PASSED ============================================================== cd pme/distance && ./Run.dist_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/distance_COM && ./Run.distCOM_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/jar_torsion && ./Run.jar_torsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_pbc.dat.save with jartorsion_pbc.dat PASSED ============================================================== cd pme/jar_distance && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing dist_pbc_vs_t.save with dist_pbc_vs_t PASSED ============================================================== cd pme/jar_distance_COM && ./Run.jar_pbc diffing mdout.save with mdout PASSED ============================================================== diffing distCOM_pbc_vs_t.save with distCOM_pbc_vs_t PASSED ============================================================== cd pme/nmropt_1_torsion && ./Run.nmropt_1_torsion diffing mdout.save with mdout PASSED ============================================================== diffing torsion_pbc.dat.save with torsion_pbc.dat PASSED ============================================================== cd pme/tautp && ./Run.nmropt_1tautp_pbc ./Run.nmropt_1tautp_pbc: 42: [: sander: unexpected operator diffing mdout.save with mdout PASSED ============================================================== cd pme/temp && ./Run.nmropt_1temp_pbc diffing mdout.save with mdout PASSED ============================================================== cd gb/2xangle && ./Run.nmropt_1_2xangle_gb diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_gb_vs_t.save with 2xangle_gb_vs_t PASSED ============================================================== cd gb/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_gb.dat.save with jartorsion_com_gb.dat PASSED ============================================================== cd gb/jar_lcod && ./Run.lcod_jar diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/jar_lcod_dist && ./Run.jar_lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod && ./Run.lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd gb/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_gb.dat.save with 2xtorsion_gb.dat PASSED ============================================================== cd pme/2xangle && ./Run.nmropt_1_2xangle_pbc diffing mdout.save with mdout PASSED ============================================================== diffing 2xangle_pbc_vs_t.save with 2xangle_pbc_vs_t PASSED ============================================================== cd pme/jar_comtorsion && ./Run.jar_comtorsion diffing mdout.save with mdout PASSED ============================================================== diffing jartorsion_com_pbc.dat.save with jartorsion_com_pbc.dat PASSED ============================================================== cd pme/jar_lcod && ./Run.jar_lcod diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/jar_lcod_dist && ./Run.lcod_dist diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod && ./Run.lcod_pme diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/lcod_com && ./Run.lcod_com diffing mdout.save with mdout PASSED ============================================================== diffing lcod_vs_t.dat.save with lcod_vs_t.dat PASSED ============================================================== cd pme/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion diffing mdout.save with mdout PASSED ============================================================== diffing 2xtorsion_pbc.dat.save with 2xtorsion_pbc.dat PASSED ============================================================== make[3]: Leaving directory `/home/anwesha/amber14/test/nmropt' cd lj_12-6-4 && ./Run.12-6-4 diffing mdout.save with mdout PASSED ============================================================== cd gb_rna && ./Run.gbrna diffing mdout.gbrna.save with mdout.gbrna PASSED ============================================================== cd gb_rna && ./Run.gbrna.min diffing mdout.gbrna.min.save with mdout.gbrna.min PASSED ============================================================== cd gb_rna && ./Run.gbrna.ln diffing mdout.gbrna.ln.save with mdout.gbrna.ln PASSED ============================================================== cd gb_rna && ./Run.gbrna.ips diffing mdout.gbrna.ips.save with mdout.gbrna.ips PASSED ============================================================== cd gbsa_xfin && ./Run.gbsa diffing mdout.gbsa.save with mdout.gbsa PASSED ============================================================== cd circ_dna && ./Run.circdna diffing mdout.circdna.save with mdout.circdna PASSED ============================================================== cd gb2_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb7_trx && ./Run.trxox && ./Run.trxox prmtop_an diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb7_trx && ./Run.trxox_md diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== cd gb8_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb8_trx && ./Run.trxox_md && ./Run.trxox_md prmtop_an diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== diffing mdout.trxox_md.save with mdout.trxox_md PASSED ============================================================== cd gbneck2nu_test && ./Run.1hji_md diffing mdout.1hji_md.save with mdout.1hji_md PASSED ============================================================== cd alpb_trx && ./Run.trxox diffing mdout.trxox.save with mdout.trxox PASSED ============================================================== cd gb1_cox2 && ./Run.cox2 diffing cox2.out.save with cox2.out PASSED ============================================================== cd LES_noPME && ./Run.LESmd SANDER: LES MD gas phase diffing md.out.save with md.out PASSED ============================================================== cd LES_noPME && ./Run.LESmd.rdiel SANDER: LES MD gas phase rdiel diffing md.rdiel.out.save with md.rdiel.out PASSED ============================================================== cd LES && ./Run.PME_LES Amber 8 ADDLES and SANDER.LES test: addles: diffing output_addles.save with output_addles PASSED ============================================================== diffing LES.crd.save with LES.crd PASSED ============================================================== diffing LES.prmtop.save with LES.prmtop PASSED ============================================================== sander.LES: diffing md.LES.out.save with md.LES.out PASSED ============================================================== cd LES_CUT && ./Run.LES Amber 10 SANDER.LES test, no PME diffing md.LES.out.save with md.LES.out PASSED ============================================================== cd LES_TEMP && ./Run.2temp SANDER: LES T coupling diffing 2temp.out.save with 2temp.out PASSED ============================================================== cd LES_GB && ./Run.LES SANDER: LES+GB 1: GB/LES GB1 diffcoords diffing les.gb1.diffcrd.out.save with les.gb1.diffcrd.out PASSED ============================================================== 1: GB/LES GB1 samecoords diffing les.gb1.samecrd.out.save with les.gb1.samecrd.out PASSED ============================================================== 1: GB/LES GB5 samecoords diffing les.gb5.samecrd.out.save with les.gb5.samecrd.out PASSED ============================================================== 1: GB/LES GB7 samecoords diffing les.gb7.samecrd.out.save with les.gb7.samecrd.out PASSED ============================================================== 1: GB/LES GB7 diffcoords w/RDT diffing les.gb7.rdt.out.save with les.gb7.rdt.out PASSED ============================================================== cd PIMD/part_pimd_water && ./Run.pimd diffing addles.out.save with addles.out PASSED ============================================================== diffing pimd.out.save with pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_water && ./Run.nmpimd diffing nmpimd.out.save with nmpimd.out PASSED ============================================================== cd PIMD/part_pimd_helium && ./Run.pimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_helium && ./Run.nmpimd diffing hef_pimd.out.save with hef_pimd.out PASSED ============================================================== cd PIMD/part_nmpimd_ntp && ./Run.nmpimd diffing ntp_nmpimd.out.save with ntp_nmpimd.out PASSED ============================================================== diffing NHC.dat.save with NHC.dat PASSED ============================================================== cd PIMD/part_pimd_spcfw && ./Run.pimd diffing spcfw_pimd.top.save with spcfw_pimd.top PASSED ============================================================== diffing spcfw_pimd.xyz.save with spcfw_pimd.xyz PASSED ============================================================== diffing spcfw_pimd.out.save with spcfw_pimd.out PASSED ============================================================== cd PIMD/part_cmd_water/equilib && ./Run.cmdyn diffing h2o_les.top.save with h2o_les.top PASSED ============================================================== diffing h2o_les.crd.save with h2o_les.crd PASSED ============================================================== diffing cmd.out.save with cmd.out PASSED ============================================================== cd PIMD/part_cmd_water/start && ./Run.cmdyn diffing cmd.out.save with cmd.out PASSED ============================================================== cd PIMD/part_cmd_water/restart && ./Run.cmdyn diffing cmd.out.save with cmd.out PASSED ============================================================== cd PIMD/part_rpmd_water && ./Run.rpmd diffing spcfw_rpmd.top.save with spcfw_rpmd.top PASSED ============================================================== diffing spcfw_rpmd.xyz.save with spcfw_rpmd.xyz PASSED ============================================================== diffing spcfw_rpmd.out.save with spcfw_rpmd.out PASSED ============================================================== cd ti_mass/pent_LES_PIMD && ./Run.pentadiene diffing addles.out.save with addles.out PASSED ============================================================== diffing pent-TI_les.top.save with pent-TI_les.top PASSED ============================================================== diffing pimd.out.save with pimd.out PASSED ============================================================== cd amoeba_wat1 && ./Run.amoeba_wat1 diffing amoeba_wat1.out.save with amoeba_wat1.out PASSED ============================================================== cd amoeba_wat2 && ./Run.amoeba_wat2 diffing amoeba_wat2.out.save with amoeba_wat2.out PASSED ============================================================== cd amoeba_wat2 && ./Run.ntpverlet diffing ntpverlet.save with ntpverlet PASSED ============================================================== cd amoeba_gb1 && ./Run.amoeba_gb1 diffing mdout.amoeba_gb1.save with mdout.amoeba_gb1 PASSED ============================================================== cd amoeba_jac && ./Run.amoeba_jac diffing amoeba_jac.mdout.save with amoeba_jac.mdout PASSED ============================================================== cd amoeba_formbox && ./Run.amoeba_formbox diffing amoeba_formbox.mdout.save with amoeba_formbox.mdout PASSED ============================================================== cd ncsu && ./run-serial.sh >>>>>>> doing 'abmd_ANALYSIS' >>>>>>> doing 'abmd_FLOODING' >>>>>>> doing 'abmd_UMBRELLA' >>>>>>> doing 'smd' diffing save/mdout with mdout PASSED ============================================================== diffing save/smd.txt with smd.txt PASSED ============================================================== >>>>>>> doing 'pmd' diffing save/mdout with mdout PASSED ============================================================== diffing save/pmd.txt with pmd.txt PASSED ============================================================== >>>>>>> doing 'smd2' diffing save/mdout with mdout PASSED ============================================================== diffing save/work.txt with work.txt PASSED ============================================================== cd sander_pbsa_dmp && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== cd sander_pbsa_ipb2 && ./Run.110D.min diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== cd sander_pbsa_delphi && ./Run.1az6.min diffing mdout.1az6.min.save with mdout.1az6.min PASSED ============================================================== cd sander_pbsa_lpb && ./Run.lsolver.min bcoption=5 solvopt=1 diffing out.save/mdout.min_bc5_solv1.save with mdout.min_bc5_solv1 PASSED ============================================================== bcoption=5 solvopt=2 diffing out.save/mdout.min_bc5_solv2.save with mdout.min_bc5_solv2 PASSED ============================================================== bcoption=5 solvopt=3 diffing out.save/mdout.min_bc5_solv3.save with mdout.min_bc5_solv3 PASSED ============================================================== bcoption=5 solvopt=4 diffing out.save/mdout.min_bc5_solv4.save with mdout.min_bc5_solv4 PASSED ============================================================== bcoption=6 solvopt=1 diffing out.save/mdout.min_bc6_solv1.save with mdout.min_bc6_solv1 PASSED ============================================================== bcoption=6 solvopt=3 diffing out.save/mdout.min_bc6_solv3.save with mdout.min_bc6_solv3 PASSED ============================================================== bcoption=6 solvopt=4 diffing out.save/mdout.min_bc6_solv4.save with mdout.min_bc6_solv4 PASSED ============================================================== cd sander_pbsa_radi && ./Run.ion.min diffing ./out.save/Na.inp1.out.save with Na.inp1.out PASSED ============================================================== diffing ./out.save/Na.inp2.out.save with Na.inp2.out PASSED ============================================================== diffing ./out.save/nma.inp1.out.save with nma.inp1.out PASSED ============================================================== diffing ./out.save/nma.inp2.out.save with nma.inp2.out PASSED ============================================================== diffing ./out.save/da.inp1.out.save with da.inp1.out PASSED ============================================================== diffing ./out.save/da.inp2.out.save with da.inp2.out PASSED ============================================================== cd sander_pbsa_tsr && ./Run.tsrb.min diffing mdout.tsrb.min.save with mdout.tsrb.min PASSED ============================================================== cd sander_pbsa_frc && ./test dbf_0.argasp checking argasp force diffing force.save with force.dat PASSED ============================================================== dbf_0.dadt checking dadt force diffing force.save with force.dat PASSED ============================================================== dbf_0.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_0.lysasp checking lysasp force diffing force.save with force.dat PASSED ============================================================== dbf_0.polyALA checking polyALA force diffing force.save with force.dat PASSED ============================================================== dbf_0.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_1.argasp checking argasp force diffing force.save with force.dat PASSED ============================================================== dbf_1.dadt checking dadt force diffing force.save with force.dat PASSED ============================================================== dbf_1.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_1.lysasp checking lysasp force diffing force.save with force.dat PASSED ============================================================== dbf_1.polyALA checking polyALA force diffing force.save with force.dat PASSED ============================================================== dbf_1.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== dbf_2.argasp checking argasp force diffing force.save with force.dat PASSED ============================================================== dbf_2.dadt checking dadt force diffing force.save with force.dat PASSED ============================================================== dbf_2.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== dbf_2.lysasp checking lysasp force diffing force.save with force.dat PASSED ============================================================== dbf_2.polyALA checking polyALA force diffing force.save with force.dat PASSED ============================================================== dbf_2.polyAT checking polyAT force diffing force.save with force.dat PASSED ============================================================== cd sander_pbsa_decres && ./Run.pbsa_decres diffing mdout.pbsa_decres.save with mdout.pbsa_decres PASSED ============================================================== cd sander_pbsa_decpw && ./Run.pbsa_decpw diffing mdout.pbsa_decpw.save with mdout.pbsa_decpw PASSED ============================================================== cd sander_pbsa_ligand && ./Run diffing mdout.lig.min.save with mdout.lig.min PASSED ============================================================== cd sander_pbsa_imin5 && ./Run.min diffing minout.save with minout PASSED ============================================================== cd cnstph/implicit && ./Run.cnstph diffing mdout.save with mdout PASSED ============================================================== diffing cpout.save with cpout PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala; fi SANDER: 3D-RISM diffing ala.out.save.totChg with ala.out.totChg PASSED ============================================================== diffing ala.out.save.rel with ala.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.mdiis0; fi SANDER: 3D-RISM diffing ala.mdiis0.out.save.totChg with ala.mdiis0.out.totChg PASSED ============================================================== diffing ala.mdiis0.out.save.rel with ala.mdiis0.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.mdiis1; fi SANDER: 3D-RISM diffing ala.mdiis1.out.save.totChg with ala.mdiis1.out.totChg PASSED ============================================================== diffing ala.mdiis1.out.save.rel with ala.mdiis1.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.resize; fi SANDER: 3D-RISM w/ Force Extrapolation & dynamic solvation box diffing ala.resize.out.save.totChg with ala.resize.out.totChg PASSED ============================================================== diffing ala.resize.out.save.rel with ala.resize.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.dist; fi SANDER: 3D-RISM: KH distributions diffing ala.dist.out.save with ala.dist.out PASSED ============================================================== diffing guv.O.5.dx.save with guv.O.5.dx PASSED ============================================================== diffing huv.H1.5.dx.save with huv.H1.5.dx PASSED ============================================================== diffing guv_dT.O.5.dx.save with guv_dT.O.5.dx PASSED ============================================================== diffing guv_dT.H1.5.dx.save with guv_dT.H1.5.dx PASSED ============================================================== diffing uuv.O.5.dx.save with uuv.O.5.dx PASSED ============================================================== diffing uuv.H1.5.dx.save with uuv.H1.5.dx PASSED ============================================================== diffing cuv_dT.O.5.dx.save with cuv_dT.O.5.dx PASSED ============================================================== diffing cuv_dT.H1.5.dx.save with cuv_dT.H1.5.dx PASSED ============================================================== diffing asympcr.5.dx.save with asympcr.5.dx PASSED ============================================================== diffing quv.5.dx.save with quv.5.dx PASSED ============================================================== diffing chgdist.5.dx.save with chgdist.5.dx PASSED ============================================================== diffing exchem.5.dx.save with exchem.5.dx PASSED ============================================================== diffing exchem.O.5.dx.save with exchem.O.5.dx PASSED ============================================================== diffing exchem.H1.5.dx.save with exchem.H1.5.dx PASSED ============================================================== diffing solvene.5.dx.save with solvene.5.dx PASSED ============================================================== diffing solvene.O.5.dx.save with solvene.O.5.dx PASSED ============================================================== diffing solvene.H1.5.dx.save with solvene.H1.5.dx PASSED ============================================================== diffing entropy.5.dx.save with entropy.5.dx PASSED ============================================================== diffing entropy.O.5.dx.save with entropy.O.5.dx PASSED ============================================================== diffing entropy.H1.5.dx.save with entropy.H1.5.dx PASSED ============================================================== diffing exchemGF.5.dx.save with exchemGF.5.dx PASSED ============================================================== diffing exchemGF.O.5.dx.save with exchemGF.O.5.dx PASSED ============================================================== diffing exchemGF.H1.5.dx.save with exchemGF.H1.5.dx PASSED ============================================================== diffing solveneGF.5.dx.save with solveneGF.5.dx PASSED ============================================================== diffing solveneGF.O.5.dx.save with solveneGF.O.5.dx PASSED ============================================================== diffing solveneGF.H1.5.dx.save with solveneGF.H1.5.dx PASSED ============================================================== diffing entropyGF.5.dx.save with entropyGF.5.dx PASSED ============================================================== diffing entropyGF.O.5.dx.save with entropyGF.O.5.dx PASSED ============================================================== diffing entropyGF.H1.5.dx.save with entropyGF.H1.5.dx PASSED ============================================================== diffing potUV.5.dx.save with potUV.5.dx PASSED ============================================================== diffing potUV.O.5.dx.save with potUV.O.5.dx PASSED ============================================================== diffing potUV.H1.5.dx.save with potUV.H1.5.dx PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.dist.xyzv; fi SANDER: 3D-RISM diffing quv.5.xyzv.trunc.save with quv.5.xyzv.trunc PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.hnc; fi SANDER: 3D-RISM diffing ala.hnc.out.save.totChg with ala.hnc.out.totChg PASSED ============================================================== diffing ala.hnc.out.save.rel with ala.hnc.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.list; fi SANDER: 3D-RISM diffing ala.list.out.save.totChg with ala.list.out.totChg PASSED ============================================================== diffing ala.list.out.save.rel with ala.list.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.pse1; fi SANDER: 3D-RISM diffing ala.pse1.out.save.totChg with ala.pse1.out.totChg PASSED ============================================================== diffing ala.pse1.out.save.rel with ala.pse1.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.min; fi SANDER: 3D-RISM diffing ala.min.out.save.totChg with ala.min.out.totChg PASSED ============================================================== diffing ala.min.out.save.rel with ala.min.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/ala && ./Run.ala.imin5; fi SANDER: 3D-RISM diffing ala.imin5.out.save.totChg with ala.imin5.out.totChg PASSED ============================================================== diffing ala.imin5.out.save.rel with ala.imin5.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph1; fi diffing ph1.out.save.totChg with ph1.out.totChg PASSED ============================================================== diffing ph1.out.save.rel with ph1.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph1.pse1; fi diffing ph1.pse1.out.save.totChg with ph1.pse1.out.totChg PASSED ============================================================== diffing ph1.pse1.out.save.rel with ph1.pse1.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph1.pse3; fi diffing ph1.pse3.out.save.totChg with ph1.pse3.out.totChg PASSED ============================================================== diffing ph1.pse3.out.save.rel with ph1.pse3.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph1-nacl; fi diffing ph1-nacl.out.save.totChg with ph1-nacl.out.totChg PASSED ============================================================== diffing ph1-nacl.out.save.rel with ph1-nacl.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph1-nacl.pse1; fi diffing ph1-nacl.pse1.out.save.totChg with ph1-nacl.pse1.out.totChg PASSED ============================================================== diffing ph1-nacl.pse1.out.save.rel with ph1-nacl.pse1.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph1-nacl.pse3; fi diffing ph1-nacl.pse3.out.save.totChg with ph1-nacl.pse3.out.totChg PASSED ============================================================== diffing ph1-nacl.pse3.out.save.rel with ph1-nacl.pse3.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph2; fi diffing ph2.out.save.totChg with ph2.out.totChg PASSED ============================================================== diffing ph2.out.save.rel with ph2.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph10; fi diffing ph10.out.save.totChg with ph10.out.totChg PASSED ============================================================== diffing ph10.out.save.rel with ph10.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph10-nacl; fi diffing ph10-nacl.out.save.totChg with ph10-nacl.out.totChg PASSED ============================================================== diffing ph10-nacl.out.save.rel with ph10-nacl.out.rel PASSED ============================================================== if [ -n "testrism" ]; then cd rism3d/phosphate && ./Run.ph20; fi diffing ph20.out.save.totChg with ph20.out.totChg PASSED ============================================================== diffing ph20.out.save.rel with ph20.out.rel PASSED ============================================================== (cd crg_reloc/water && ./Run.water.min) diffing min.out.save with min.out PASSED ============================================================== (cd crg_reloc/water && ./Run.water.md) diffing md.out.save with md.out PASSED ============================================================== cd amd && make -k test make[3]: Entering directory `/home/anwesha/amber14/test/amd' Testing AMD with PME diffing mdout.pme.amd1.save with mdout.pme.amd1 PASSED ============================================================== diffing mdout.pme.amd2.save with mdout.pme.amd2 PASSED ============================================================== diffing mdout.pme.amd3.save with mdout.pme.amd3 PASSED ============================================================== Testing AMD with IPS diffing mdout.ips.amd1.save with mdout.ips.amd1 PASSED ============================================================== diffing mdout.ips.amd2.save with mdout.ips.amd2 PASSED ============================================================== diffing mdout.ips.amd3.save with mdout.ips.amd3 PASSED ============================================================== Testing AMD with GB diffing mdout.gb.amd1.save with mdout.gb.amd1 PASSED ============================================================== diffing mdout.gb.amd2.save with mdout.gb.amd2 PASSED ============================================================== diffing mdout.gb.amd3.save with mdout.gb.amd3 PASSED ============================================================== make[3]: Leaving directory `/home/anwesha/amber14/test/amd' cd scaledMD && make -k test make[3]: Entering directory `/home/anwesha/amber14/test/scaledMD' Testing scaledMD with PME diffing mdout.save with mdout PASSED ============================================================== make[3]: Leaving directory `/home/anwesha/amber14/test/scaledMD' export TESTsander='../../bin/sander'; cd gact_ips && ./Run.ips_sgld diffing mdout.ips_sgld.save with mdout.ips_sgld PASSED ============================================================== export TESTsander='../../bin/sander'; cd gact_ips && ./Run.ips_sgldfp diffing mdout.ips_sgldfp.save with mdout.ips_sgldfp PASSED ============================================================== export TESTsander='../../bin/sander'; cd gact_ips && ./Run.ips_sgldg diffing mdout.ips_sgldg.save with mdout.ips_sgldg PASSED ============================================================== export TESTsander='../../bin/sander'; cd gact_ips && ./Run.ips_sgmdg diffing mdout.ips_sgmdg.save with mdout.ips_sgmdg PASSED ============================================================== export TESTsander='../../bin/sander'; cd gb_rna && ./Run.gbrna.sgld diffing mdout.gbrna.sgld.save with mdout.gbrna.sgld PASSED ============================================================== export TESTsander='../../bin/sander'; cd gb_rna && ./Run.gbrna.sgldfp diffing mdout.gbrna.sgldfp.save with mdout.gbrna.sgldfp PASSED ============================================================== export TESTsander='../../bin/sander'; cd gb_rna && ./Run.gbrna.sgldg diffing mdout.gbrna.sgldg.save with mdout.gbrna.sgldg PASSED ============================================================== export TESTsander='../../bin/sander'; cd gb_rna && ./Run.gbrna.sgmdg diffing mdout.gbrna.sgmdg.save with mdout.gbrna.sgmdg PASSED ============================================================== export TESTsander='../../bin/sander'; cd emap/ && ./Run.emap diffing mdout.emap.save with mdout.emap PASSED ============================================================== cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md diffing mdout.dhfr_charmm.save with mdout.dhfr_charmm PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.min diffing mdout.dhfr_charmm_noshake.min.save with mdout.dhfr_charmm_noshake.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.md diffing mdout.dhfr_charmm_noshake.md.save with mdout.dhfr_charmm_noshake.md PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.min diffing mdout.dhfr_charmm.min.save with mdout.dhfr_charmm.min PASSED ============================================================== cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.md diffing mdout.dhfr_charmm.md.save with mdout.dhfr_charmm.md PASSED ============================================================== cd nmode && ./Run.ala-dipeptide NMODE: find normal modes diffing vibs.out.save with vibs.out PASSED ============================================================== NMODE: find Langevin modes diffing lvibs.out.save with lvibs.out PASSED ============================================================== diffing lmode.head.save with lmode.head PASSED ============================================================== cd nmode && ./Run.ala-dipeptide_rgroup NMODE: find normal modes, with a restraint weighting diffing vibsr.out.save with vibsr.out PASSED ============================================================== cd newton_raph && ./Run.newton_raph diffing nmd_min.out.save with nmd_min.out PASSED ============================================================== cd qmmm2/input_validation && ./Run.invalid_atom_ids diffing invalid_atom_ids.out.save with invalid_atom_ids.out PASSED ============================================================== cd qmmm2/input_validation && ./Run.non_unique_qm_atoms diffing non-unique.out.save with non-unique.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_0 diffing nma_md_diag_routine_0.out.save with nma_md_diag_routine_0.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_2 diffing nma_md_diag_routine_2.out.save with nma_md_diag_routine_2.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_3 diffing nma_md_diag_routine_3.out.save with nma_md_diag_routine_3.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_4 diffing nma_md_diag_routine_4.out.save with nma_md_diag_routine_4.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_5 diffing nma_md_diag_routine_5.out.save with nma_md_diag_routine_5.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_6 diffing nma_md_diag_routine_6.out.save with nma_md_diag_routine_6.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_7 diffing nma_md_diag_routine_7.out.save with nma_md_diag_routine_7.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb0 diffing nma_md_qmgb0.out.save with nma_md_qmgb0.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb1 diffing nma_md_qmgb1.out.save with nma_md_qmgb1.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb2 diffing nma_md_qmgb2.out.save with nma_md_qmgb2.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb2_saltcon diffing nma_md_qmgb2_saltcon.out.save with nma_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb3 diffing nma_md_qmgb3.out.save with nma_md_qmgb3.out PASSED ============================================================== cd qmmm2/pure_QM_MD && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_shake && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_tight_p && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_tight_p && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3_08 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGPM3_08 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1 && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1_ADDMM && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_AM1_ADDMM && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_RM1 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_RM1 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_RM1 && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_MNDO && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_MNDO && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_MNDO && ./Run.C6H4FCL_md diffing C6H4FCL_md.out.save with C6H4FCL_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PM6 && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_PM6 && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md diffing nma_md.out.save with nma_md.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb0 diffing nma_md_qmgb0.out.save with nma_md_qmgb0.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb2 diffing nma_md_qmgb2.out.save with nma_md_qmgb2.out PASSED ============================================================== cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb2_saltcon diffing nma_md_qmgb2_saltcon.out.save with nma_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/1-2-ethanediol_PM3CARB1 && ./Run.PM3CARB1_md diffing ethanediol_md.out.save with ethanediol_md.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_qmmm_int0 diffing lysine_md_qmmm_int0.out.save with lysine_md_qmmm_int0.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_qmmm_int2 diffing lysine_md_qmmm_int2.out.save with lysine_md_qmmm_int2.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_lnk_dis_neg diffing lysine_md_lnk_dis_neg.out.save with lysine_md_lnk_dis_neg.out PASSED ============================================================== cd qmmm2/lysine_PM3 && ./Run.lysine_md_lnk_method2 diffing lysine_md_lnk_method_2.out.save with lysine_md_lnk_method_2.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb0 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb0 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb2 diffing lysine_md_igb2.out.save with lysine_md_igb2.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb5 diffing lysine_md_igb5.out.save with lysine_md_igb5.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb7 diffing lysine_md_igb7.out.save with lysine_md_igb7.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_adjust_q1 diffing lysine_md_adjust_q1.out.save with lysine_md_adjust_q1.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_adjust_q2 diffing lysine_md_adjust_q2.out.save with lysine_md_adjust_q2.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_lnk_dis_neg diffing lysine_md_lnk_dis_neg.out.save with lysine_md_lnk_dis_neg.out PASSED ============================================================== cd qmmm2/lysine_PM3_qmgb2_alpb && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_mulliken && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_mulliken && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine_qmmm diffing lysine_qmmm.out.save with lysine_qmmm.out PASSED ============================================================== cd qmmm2/lysine_AM1 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_AM1 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_MNDO && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_MNDO && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/lysine_PM6 && ./Run.lysine diffing lysine.out.save with lysine.out PASSED ============================================================== cd qmmm2/lysine_PM6 && ./Run.lysine_md diffing lysine_md.out.save with lysine_md.out PASSED ============================================================== cd qmmm2/meoh-nh3_PM6-DH+ && ./Run.meoh-nh3 diffing meoh-nh3_opt.out.save with meoh-nh3_opt.out PASSED ============================================================== cd qmmm2/meoh-nh3_PM6-DH+ && ./Run.meoh-nh3_md diffing meoh-nh3_md.out.save with meoh-nh3_md.out PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.water_dimer.x diffing water_dimer.out.save with water_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.ammonia_dimer.x diffing ammonia_dimer.out.save with ammonia_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.formic_acid_dimer.x diffing formic_acid_dimer.out.save with formic_acid_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.water_dimer.x diffing water_dimer.out.save with water_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.ammonia_dimer.x diffing ammonia_dimer.out.save with ammonia_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.formic_acid_dimer.x diffing formic_acid_dimer.out.save with formic_acid_dimer.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.methanethiol.x diffing methanethiol_water.out.save with methanethiol_water.out PASSED ============================================================== cd qmmm2/znme2/ && ./Run.min diffing znme2.znb.min.out.save with znme2.znb.min.out PASSED ============================================================== cd qmmm2/znme2/ && ./Run.md diffing znme2.znb.md.out.save with znme2.znb.md.out PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod.min diffing mndod.min.mdout.save with mndod.min.mdout PASSED ============================================================== diffing mndod.min.mdcrd.save with mndod.min.mdcrd PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod.md diffing mndod.md.mdout.save with mndod.md.mdout PASSED ============================================================== diffing mndod.md.mdcrd.save with mndod.md.mdcrd PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod-mm.min diffing mndod-mm.min.mdout.save with mndod-mm.min.mdout PASSED ============================================================== diffing mndod-mm.min.mdcrd.save with mndod-mm.min.mdcrd PASSED ============================================================== cd qmmm2/cysdip/ && ./Run.mndod-mm.md diffing mndod-mm.md.mdout.save with mndod-mm.md.mdout PASSED ============================================================== diffing mndod-mm.md.mdcrd.save with mndod-mm.md.mdcrd PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_imaged diffing mdout.oct_nma_imaged.save with mdout.oct_nma_imaged PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_noimage diffing mdout.oct_nma_noimage.save with mdout.oct_nma_noimage PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0 diffing mdout.ortho_qmewald0.save with mdout.ortho_qmewald0 PASSED ============================================================== cd qmmm2/xcrd_build_test/ && ./Run.truncoct_qmewald0 diffing mdout.truncoct_qmewald0.save with mdout.truncoct_qmewald0 PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_calc_mulliken diffing crambin_md_calc_mulliken.out.save with crambin_md_calc_mulliken.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2 diffing crambin_md_qmgb2.out.save with crambin_md_qmgb2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_alpb diffing crambin_md_qmgb2_alpb.out.save with crambin_md_qmgb2_alpb.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq1 diffing crambin_md_qmgb2_aq1.out.save with crambin_md_qmgb2_aq1.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq2 diffing crambin_md_qmgb2_aq2.out.save with crambin_md_qmgb2_aq2.out PASSED ============================================================== cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_saltcon diffing crambin_md_qmgb2_saltcon.out.save with crambin_md_qmgb2_saltcon.out PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_internal diffing mdout.1NLN_internal.save with mdout.1NLN_internal PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspev diffing mdout.1NLN_dspev.save with mdout.1NLN_dspev PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevd diffing mdout.1NLN_dspevd.save with mdout.1NLN_dspevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevx diffing mdout.1NLN_dspevx.save with mdout.1NLN_dspevx PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyev diffing mdout.1NLN_dsyev.save with mdout.1NLN_dsyev PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevd diffing mdout.1NLN_dsyevd.save with mdout.1NLN_dsyevd PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevr diffing mdout.1NLN_dsyevr.save with mdout.1NLN_dsyevr PASSED ============================================================== cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_auto diffing mdout.1NLN_auto.save with mdout.1NLN_auto PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_min diffing mdout.1NLN_min.save with mdout.1NLN_min PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1 diffing mdout.1NLN_MD_ntb1.save with mdout.1NLN_MD_ntb1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq1 diffing mdout.1NLN_MD_ntb1_aq1.save with mdout.1NLN_MD_ntb1_aq1 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2 diffing mdout.1NLN_MD_ntb1_aq2.save with mdout.1NLN_MD_ntb1_aq2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_mmcorr diffing mdout.1NLN_MD_ntb1_mmcorr.save with mdout.1NLN_MD_ntb1_mmcorr PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_qmewald2 diffing mdout.1NLN_MD_ntb1_qmewald2.save with mdout.1NLN_MD_ntb1_qmewald2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb2 diffing mdout.1NLN_MD_ntb2.save with mdout.1NLN_MD_ntb2 PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2_NUMER_DERIV diffing mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV.save with mdout.1NLN_MD_ntb1_aq2_NUMER_DERIV PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_dis_neg diffing mdout.1NLN_MD_ntb1_lnk_dis_neg.save with mdout.1NLN_MD_ntb1_lnk_dis_neg PASSED ============================================================== cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_method2 diffing mdout.1NLN_MD_ntb1_lnk_method2.save with mdout.1NLN_MD_ntb1_lnk_method2 PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged diffing mdout.notimaged.save with mdout.notimaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md diffing mdout.notimaged_md.save with mdout.notimaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme diffing mdout.notimaged_md_pme.save with mdout.notimaged_md_pme PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald diffing mdout.notimaged_md_pme_qmewald.save with mdout.notimaged_md_pme_qmewald PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald_lowmem diffing mdout.notimaged_md_pme_qmewald_lowmem.save with mdout.notimaged_md_pme_qmewald_lowmem PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged diffing mdout.imaged.save with mdout.imaged PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged_md diffing mdout.imaged_md.save with mdout.imaged_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center diffing mdout.img_center.save with mdout.img_center PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_md diffing mdout.img_center_md.save with mdout.img_center_md PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_bigqmcut_md diffing mdout.img_center_bigqmcut_md.save with mdout.img_center_bigqmcut_md PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md_hot_start diffing crambin_md_hot_start.out.save with crambin_md_hot_start.out PASSED ============================================================== cd qmmm2/crambin && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap diffing tip3p_cap.out.save with tip3p_cap.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md diffing tip3p_cap_md.out.save with tip3p_cap_md.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake diffing tip3p_cap_md_shake.out.save with tip3p_cap_md_shake.out PASSED ============================================================== cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake_qmshakeoff diffing tip3p_cap_md_shake_qmshake_off.out.save with tip3p_cap_md_shake_qmshake_off.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_lowmem && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM diffing MG_QM_water_MM.out.save with MG_QM_water_MM.out PASSED ============================================================== cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM_MD diffing MG_QM_water_MM_MD.out.save with MG_QM_water_MM_MD.out PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.mg_periodic_vsolv_wat diffing mg_periodic_vsolv_wat.out.save with mg_periodic_vsolv_wat.out PASSED ============================================================== cd qmmm2/variable_solvent && ./Run.1NLN_MD_ntb1_vsolv diffing mdout.1NLN_MD_ntb1_vsolv.save with mdout.1NLN_MD_ntb1_vsolv PASSED ============================================================== cd qmmm2/PM3-MMX && ./Run.crambin_md_pm3mmx diffing crambin_md_pm3mmx.out.save with crambin_md_pm3mmx.out PASSED ============================================================== cd qmmm2/PM3-MMX2 && ./Run.crambin_md_pm3mmx2 diffing crambin_md_pm3mmx2.out.save with crambin_md_pm3mmx2.out PASSED ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin diffing crambin.out.save with crambin.out PASSED ============================================================== cd qmmm2/crambin_PM6 && ./Run.crambin_md diffing crambin_md.out.save with crambin_md.out PASSED ============================================================== diffing mdcrd.save with mdcrd PASSED ============================================================== diffing mdvel.save with mdvel PASSED ============================================================== diffing restrt.save with restrt PASSED ============================================================== cd qmmm2/PM3-MAIS && ./Run.zundel diffing zundel.mdout.save with zundel.mdout PASSED ============================================================== diffing zundel.mdcrd.save with zundel.mdcrd PASSED ============================================================== cd qmmm2/PM3-MAIS && ./Run.hcl_wat diffing hcl_wat.mdout.save with hcl_wat.mdout PASSED ============================================================== diffing hcl_wat.mdcrd.save with hcl_wat.mdcrd PASSED ============================================================== cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_PDDGPM3 diffing mdout.MechEm_PDDGPM3.save with mdout.MechEm_PDDGPM3 PASSED ============================================================== cd qmmm2/qmmm_switching_func && ./Run.nma_md_switching diffing nma.out.save with nma.out PASSED ============================================================== cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb0 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2_saltcon DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_disp DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_shake_DFTB && ./Run.nma_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_dis_neg DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_method2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_qmmm_int0 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb5 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb7 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_qmgb2_alpb && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/water && ./Run.water DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/water && ./Run.water_read_mdin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/water && ./Run.water_read_file DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md_hot_start DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_calc_mulliken DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_alpb DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_saltcon DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_link_atoms DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_telec DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM_MD DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme_qmewald DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_bigqmcut_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut_lowmem && ./Run.MG_QM_water_MM_MD DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake_qmshakeoff DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_min DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_dis_neg DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_method2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1_disp DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_qmewald2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb2 DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA DFTB SLKO files not found - Skipping Test... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR DFTB SLKO files not found - Skipping Test... cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_DFTB DFTB SLKO files not found - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF dftb executable is called dftb.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb_md ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF dftb executable is called dftb.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz_md ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.template.lda-sz ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g_md GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.template.bp86_6-31g GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g_md TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.template.blyp_6-31g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g09 or g03 cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g_md GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g09 or g03 cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.template.blyp_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g09 or g03 cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g_md Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.template.blyp_6-31g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g_md NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.template.blyp_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.blyp_6-31g_md Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_ADF && ./Run.aladip.blyp_dz.MechEm ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/QMMM_MD_ADF && ./Run.nma-spcfw-15.blyp_dz.MechEm ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g.MechEm Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g.MechEm TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g.MechEm TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.aladip.hf_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g09 or g03 cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.nma-spcfw-15.hf_sto-3g GAUSSIAN not installed - Skipping Test... Check your GAUSSIAN installation and make sure that the GAUSSIAN executable is called g09 or g03 cd qmmm_EXTERN/QMMM_MD_NWChem && ./Run.aladip.hf_sto-3g NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.aladip.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.aladip.hf_sto-3g.MechEm Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.nma-spcfw-15.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_Lio/water && ./Run.water Lio is not installed - Skipping Test... Check your Lio installation and the LIOHOME environment setting cd qmmm_EXTERN/QMMM_Lio/water && ./Run.td.water Lio is not installed - Skipping Test... Check your Lio installation and the LIOHOME environment setting cd abfqmmm/abfqmmm_water_sp && ./Run.abfqmmm_water_sp diffing abfqmmm_water_sp.out.save with abfqmmm_water_sp.out PASSED ============================================================== diffing abfqmmm_water_sp.frc.save with abfqmmm_water_sp.frc PASSED ============================================================== diffing abfqmmm_water_sp.pdb.save with abfqmmm_water_sp.pdb PASSED ============================================================== diffing abfqmmm_water_sp.idrst.save with abfqmmm_water_sp.idrst PASSED ============================================================== cd abfqmmm/abfqmmm_water_md && ./Run.abfqmmm_water_md diffing abfqmmm_water_md.out.save with abfqmmm_water_md.out PASSED ============================================================== diffing abfqmmm_water_md.frc.save with abfqmmm_water_md.frc PASSED ============================================================== diffing abfqmmm_water_md.pdb.save with abfqmmm_water_md.pdb PASSED ============================================================== diffing abfqmmm_water_md.idrst.save with abfqmmm_water_md.idrst PASSED ============================================================== cd abfqmmm/abfqmmm_dmpoh_md && ./Run.abfqmmm_dmpoh_md diffing abfqmmm_dmpoh_md.out.save with abfqmmm_dmpoh_md.out PASSED ============================================================== diffing abfqmmm_dmpoh_md.frc.save with abfqmmm_dmpoh_md.frc PASSED ============================================================== diffing abfqmmm_dmpoh_md.pdb.save with abfqmmm_dmpoh_md.pdb PASSED ============================================================== diffing abfqmmm_dmpoh_md.idrst.save with abfqmmm_dmpoh_md.idrst PASSED ============================================================== diffing abfqmmm_dmpoh_md.rst.save with abfqmmm_dmpoh_md.rst PASSED ============================================================== cd abfqmmm/abfqmmm_lysozyme_md && ./Run.abfqmmm_lysozyme_md diffing abfqmmm_lysozyme_md.out.save with abfqmmm_lysozyme_md.out PASSED ============================================================== diffing abfqmmm_lysozyme_md.frc.save with abfqmmm_lysozyme_md.frc PASSED ============================================================== diffing abfqmmm_lysozyme_md.pdb.save with abfqmmm_lysozyme_md.pdb PASSED ============================================================== diffing abfqmmm_lysozyme_md.idrst.save with abfqmmm_lysozyme_md.idrst PASSED ============================================================== cd abfqmmm/adqmmm_water_md && ./Run.adqmmm_water_md diffing adqmmm_water_md.out.save with adqmmm_water_md.out PASSED ============================================================== diffing adqmmm_water_md.frc.save with adqmmm_water_md.frc PASSED ============================================================== diffing adqmmm_water_md.pdb.save with adqmmm_water_md.pdb PASSED ============================================================== diffing adqmmm_water_md.idrst.save with adqmmm_water_md.idrst PASSED ============================================================== cd abfqmmm/hotspot_water_md && ./Run.hotspot_water_md diffing hotspot_water_md.out.save with hotspot_water_md.out PASSED ============================================================== diffing hotspot_water_md.frc.save with hotspot_water_md.frc PASSED ============================================================== diffing hotspot_water_md.pdb.save with hotspot_water_md.pdb PASSED ============================================================== diffing hotspot_water_md.idrst.save with hotspot_water_md.idrst PASSED ============================================================== cd sebomd/AM1/dimethylether && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1/methionine && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1/nucleoside && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1/water1 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1D/dimethylether && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1D/methionine && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1D/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1D/nucleoside && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/AM1D/water1 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/DC/water32 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/Ewald-CM1/Water2 && ./md.csh diffing md.save with md.out PASSED ============================================================== cd sebomd/Ewald-ConstantCharge/Water2 && ./md.csh diffing md.save with md.out PASSED ============================================================== cd sebomd/Ewald-Mulliken/Water2 && ./md.csh diffing md.save with md.out PASSED ============================================================== cd sebomd/MinimumImage/Water2 && ./md.csh diffing md.save with md.out PASSED ============================================================== cd sebomd/method3/alaninedipeptide && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/method3/ethanol_and_water && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/MNDO/dimethylether && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/MNDO/methionine && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/MNDO/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/MNDO/nucleoside && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/MNDO/water1 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/RM1/dimethylether && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/RM1/methionine && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/RM1/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/RM1/nucleoside && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/RM1/water1 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PIF2/dimethylether && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PIF2/water1 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PIF2/doublewater && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PIF2/ethanol_and_water && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PIF3/water1 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PIF3/doublewater && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PIF3/ethanol_and_water && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PM3/alaninedipeptide && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PM3/dimethylether && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PM3/methionine && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PM3/n-methyl-acetamide && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PM3/nucleoside && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== cd sebomd/PM3/water1 && ./min.csh && ./md.csh diffing min.save with min.out PASSED ============================================================== diffing md.save with md.out PASSED ============================================================== export TESTsander='../../../bin/sander'; unset DO_PARALLEL; cd emil/emil_sander_gbsa && ./Run.emil EMIL DO_PARALLEL not set... testing emil in serial. diffing mdout.emil.0.0.save with mdout.emil.0.0 PASSED ============================================================== diffing emil.log.0.0.save with emil.log.0.0 PASSED ============================================================== diffing mdout.emil.0.1.save with mdout.emil.0.1 PASSED ============================================================== diffing emil.log.0.1.save with emil.log.0.1 PASSED ============================================================== diffing mdout.emil.0.9.save with mdout.emil.0.9 PASSED ============================================================== diffing emil.log.0.9.save with emil.log.0.9 PASSED ============================================================== export TESTsander='../../../bin/sander'; unset DO_PARALLEL; cd emil/emil_sander_tip3p && ./Run.emil EMIL DO_PARALLEL not set... testing emil in serial. diffing mdout.emil.0.1.save with mdout.emil.0.1 PASSED ============================================================== diffing emil.log.0.1.save with emil.log.0.1 PASSED ============================================================== diffing mdout.emil.0.5.save with mdout.emil.0.5 PASSED ============================================================== diffing emil.log.0.5.save with emil.log.0.5 PASSED ============================================================== diffing mdout.emil.0.9.save with mdout.emil.0.9 PASSED ============================================================== diffing emil.log.0.9.save with emil.log.0.9 PASSED ============================================================== cd sanderapi && make test make[3]: Entering directory `/home/anwesha/amber14/test/sanderapi' Testing the Fortran API gfortran -I/home/anwesha/amber14/include -L/home/anwesha/amber14/lib test.F90 -o testf -lsander /home/anwesha/amber14/bin/parmed.py -Oen -i prepare.pmd > /dev/null Traceback (most recent call last): File "/home/anwesha/amber14/bin/parmed.py", line 16, in from ParmedTools.logos import Logo ImportError: No module named ParmedTools.logos make[3]: *** [test.parm7] Error 1 Testing the Fortran file-less API gfortran -I/home/anwesha/amber14/include -L/home/anwesha/amber14/lib test2.F90 -o testf2 -lsander Running testf2 Testing GB sander interface PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the QM/MM non-periodic interface PASSED ============================================================== Testing the QM/MM periodic interface (PM3-PDDG) PASSED ============================================================== Testing the C API gcc -I/home/anwesha/amber14/include -L/home/anwesha/amber14/lib test.c -o testc -lsander Testing the C++ API g++ -I/home/anwesha/amber14/include -L/home/anwesha/amber14/lib test.cpp -o testcpp -lsander /bin/rm -f test.parm6 testf testf2 testc testcpp gake[3]: Target.serial' not remade because of errors.`test' not remade because of errors. make[3]: Leaving directory `/home/anwesha/amber14/test/sanderapi' make[2]: [test.serial.sanderapi] Error 2 (ignored) cd sanderlesapi && make test make[3]: Entering directory `/home/anwesha/amber14/test/sanderlesapi' Testing the Fortran LES API gfortran -I/home/anwesha/amber14/include -L/home/anwesha/amber14/lib test.F90 -o testf -lsanderles ./testf && /bin/rm -f testf Testing GB sander interface (diffcoords w/ RDT) PASSED ============================================================== Testing GB sander interface (samecoords w/out RDT) PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the C LES API gcc -I/home/anwesha/amber14/include -L/home/anwesha/amber14/lib test.c -o testc -lsanderles (./testc && /bin/rm -f testc) || echo "Program error" Testing GB sander interface (diffcoords w/ RDT) PASSED ============================================================== Testing GB sander interface (samecoords w/out RDT) PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the C++ LES API g++ -I/home/anwesha/amber14/include -L/home/anwesha/amber14/lib test.cpp -o testcpp -lsanderles (./testcpp && /bin/rm -f testcpp) || echo "Program error" Testing GB sander interface (diffcoords w/ RDT) PASSED ============================================================== Testing GB sander interface (samecoords w/out RDT) PASSED ============================================================== Testing PME sander interface PASSED ============================================================== Testing the Python LES API (/usr/bin/python2.7 test.py) || echo "Program error" Could not import sanderles. Skipping test make[3]: Leaving directory `/home/anwesha/amber14/test/sanderlesapi' make[2]: Leaving directory `/home/anwesha/amber14/test' make[2]: Entering directory `/home/anwesha/amber14/AmberTools/test' Finished test suite for AmberTools at Tue Jun 30 18:27:59 IST 2015. make[2]: Leaving directory `/home/anwesha/amber14/AmberTools/test' 1298 file comparisons passed 8 file comparisons failed 2 tests experienced errors Test log file saved as /home/anwesha/amber14/logs/test_at_serial/2015-06-30_17-24-33.log Test diffs file saved as /home/anwesha/amber14/logs/test_at_serial/2015-06-30_17-24-33.diff