make[1]: Entering directory `/home/msafi/amber11/AmberTools/test' ./test_at_clean.sh cd mmpbsa_py && make -k clean make[2]: Entering directory `/home/msafi/amber11/AmberTools/test/mmpbsa_py' cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 02_Poisson_Boltzmann && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 03_Alanine_Scanning && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 04_Per_Residue_Decomp && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 05_Pairwise_Decomp && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 06_NAB_Nmode && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 07_Comprehensive && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif cd 08_Stability && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif cd 09_APBS_Poisson_Boltzmann && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 10_QM_MMGBSA && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif cd 11_3D-RISM && /home/msafi/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif make[2]: Leaving directory `/home/msafi/amber11/AmberTools/test/mmpbsa_py' cd cpptraj && make -k clean make[2]: Entering directory `/home/msafi/amber11/AmberTools/test/cpptraj' Cleaning all test directories: (find . -name 'test.out' -o -name 'valgrind.out' -o -name 'Thread.*' \ -o -name 'Test_Results.dat' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) make test.all OPT=clean make[3]: Entering directory `/home/msafi/amber11/AmberTools/test/cpptraj' make[3]: Leaving directory `/home/msafi/amber11/AmberTools/test/cpptraj' make bench.all OPT=clean make[3]: Entering directory `/home/msafi/amber11/AmberTools/test/cpptraj' make[3]: Leaving directory `/home/msafi/amber11/AmberTools/test/cpptraj' make[2]: Leaving directory `/home/msafi/amber11/AmberTools/test/cpptraj' cd nab && make -k testrism make[2]: Entering directory `/home/msafi/amber11/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 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 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 tprmtop1 PASSED ============================================================== Running test to create a simple mmCIF file diffing gbrna.cif.check with gbrna.cif 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 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 huv.O.4.dx.check with huv.O.4.dx PASSED ============================================================== diffing cuv.O.4.dx.check with cuv.O.4.dx PASSED ============================================================== diffing guv.H1.4.dx.check with guv.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 ============================================================== 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 with rismion.out 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 with rismion.noasymp.out PASSED ============================================================== Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) diffing rismion_pse1.out.check with rismion_pse1.out PASSED ============================================================== Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) diffing rismion_pse3.out.check with rismion_pse3.out 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 to do basic MD (librism) (trajectory processing using the 3D-RISM command line interface) diffing rism3d.snglpnt.out.check with rism3d.snglpnt.out 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 with rism3d.snglpnt.2.out 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 ============================================================== make[2]: Leaving directory `/home/msafi/amber11/AmberTools/test/nab' cd ptraj_rmsa && ./Run.rms diffing rms.dat.save with rms.dat PASSED ============================================================== cd ptraj_rms && ./Run.rms ptraj: test rms and 2drms commands diffing rms_fit.dat.save with rms_fit.dat PASSED ============================================================== diffing rms_nofit.dat.save with rms_nofit.dat PASSED ============================================================== diffing rms2d.ps.save with rms2d.ps PASSED ============================================================== cd ptraj_matrix && ./Run.matrix ptraj: analyze fluctuation matrices diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat PASSED ============================================================== cd ptraj_order && ./Run.order ptraj: calculate S^2 parameters and relaxation rates via IRED matrix diffing orderparam.save with orderparam PASSED ============================================================== diffing noe.save with noe PASSED ============================================================== cd ptraj_trajectory && ./Run.ptraj ptraj: Test processing of trajectories with offsets and compression. diffing rem.crd.combined.save with rem.crd.combined PASSED ============================================================== diffing rem.crd.combined.save with gzip.rem.crd.combined PASSED ============================================================== diffing rem.crd.combined.save with bzip2.rem.crd.combined PASSED ============================================================== cd ptraj_remd_netcdf && ./Run.ptraj netcdf.mod ptraj: Test processing of REMD trajectories. diffing dist.crd.dat.save with dist.crd.dat PASSED ============================================================== ptraj: Test processing of NetCDF REMD trajectories. diffing dist.dat.save with dist.dat PASSED ============================================================== cd ptraj_comprehensive && ./Run.comprehensive netcdf.mod ptraj: Test multiple ptraj actions. diffing dist_end_to_end.list.save with dist_end_to_end.list PASSED ============================================================== diffing omega.save with omega PASSED ============================================================== diffing phi.save with phi PASSED ============================================================== diffing psi.save with psi PASSED ============================================================== diffing watershell.list.save with watershell.list PASSED ============================================================== diffing test.mdcrd.save with test.mdcrd PASSED ============================================================== testing NetCDF... diffing trajectory.mdcrd with trajectory_test.mdcrd PASSED ============================================================== cd cpptraj && make -k test make[2]: Entering directory `/home/msafi/amber11/AmberTools/test/cpptraj' make test.all make[3]: Entering directory `/home/msafi/amber11/AmberTools/test/cpptraj' ************************************************************** TEST: /home/msafi/amber11/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.rst7.103.save with Restart/test.rst7.103 PASSED ============================================================== diffing test.nc.save with test.nc 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/msafi/amber11/AmberTools/test/cpptraj/Test_Strip CPPTRAJ: One frame strip command test. diffing dummy.pdb.save with dummy.pdb PASSED ============================================================== diffing dummy.rst7.1.save with dummy.rst7.1 PASSED ============================================================== diffing strip.ChainA-tip3p.parm7.save with strip.ChainA-tip3p.parm7 PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_Strip CPPTRAJ: Unstrip (Lig/Rec/Complex) command test. diffing strip.ChainA-tip3p.parm7.save with complex.ChainA-tip3p.parm7 PASSED ============================================================== diffing receptor.ChainA-tip3p.parm7.save with receptor.ChainA-tip3p.parm7 PASSED ============================================================== diffing ligand.ChainA-tip3p.parm7.save with ligand.ChainA-tip3p.parm7 PASSED ============================================================== diffing Ligand.crd.save with Ligand.crd PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Broken Traj: Running broken trajectory. diffing goodrmsd.dat with badrmsd.dat PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/ptraj_trajectory 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/msafi/amber11/AmberTools/test/cpptraj/ptraj_remd_netcdf 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 ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_trajout_framerange CPPTRAJ: Trajout Frame Range 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 ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. diffing PerResRMSD.dat.save with PerResRMSD.dat PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. diffing dssp.dat.save with dssp.dat PASSED ============================================================== diffing dssp.sum.agr.save with dssp.sum.agr PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_Hbond CPPTRAJ: Hbond command test. diffing nhb.dat.save with nhb.dat PASSED ============================================================== diffing avghb.dat.save with avghb.dat PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/ptraj_comprehensive CPPTRAJ: PTRAJ comprehensive tests. diffing cpptraj.phi.save with phi PASSED ============================================================== diffing cpptraj.psi.save with psi PASSED ============================================================== diffing cpptraj.omega.save with omega PASSED ============================================================== diffing cpptraj.dist_end_to_end.list.save with dist_end_to_end.list PASSED ============================================================== diffing cpptraj.test.mdcrd.save with test.mdcrd PASSED ============================================================== CPPTRAJ: PTRAJ comprehensive mdcrd -> netcdf test. CPPTRAJ: PTRAJ comprehensive netcdf -> mdcrd test. diffing ../../ptraj_comprehensive/trajectory.mdcrd with trajectory_test.mdcrd PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_Surf CPPTRAJ: Surface calculation test. diffing surf.dat.save with surf.dat PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/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/msafi/amber11/AmberTools/test/cpptraj/Test_Mask CPPTRAJ: Mask command test. diffing mask.out.save with mask.out PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_RMSD CPPTRAJ: RMSD Test. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== CPPTRAJ: RMSD test with mass weighting. diffing rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. diffing L01.mol2.1.save with L01.mol2 PASSED ============================================================== diffing trpcage.mol2.1.save with trpcage.mol2 PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_NAstruct CPPTRAJ: NAstruct command test. diffing BP.nastruct.dat.save with BP.nastruct.dat PASSED ============================================================== diffing BPstep.nastruct.dat.save with BPstep.nastruct.dat PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/AmberTools/test/cpptraj/Test_Pucker CPPTRAJ: Pucker command test (Altona & Sundaralingam) diffing pucker.dat.save with pucker.dat PASSED ============================================================== CPPTRAJ: Pucker command test (Cremer & Pople) diffing pucker2.dat.save with pucker2.dat PASSED ============================================================== ************************************************************** TEST: /home/msafi/amber11/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.ChainA-tip3p.parm7.save with closest.ChainA-tip3p.parm7 PASSED ============================================================== make[3]: Leaving directory `/home/msafi/amber11/AmberTools/test/cpptraj' make[2]: Leaving directory `/home/msafi/amber11/AmberTools/test/cpptraj' cd antechamber/top2mol2 && ./Run.top2mol2 diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing dna.mol2.save with dna.mol2 PASSED ============================================================== diffing dna_wat.mol2.save with dna_wat.mol2 PASSED ============================================================== diffing aa.mol2.save with aa.mol2 PASSED ============================================================== cd antechamber/database && ./Run.database diffing total.frcmod.save with total.frcmod PASSED ============================================================== diffing total.prepi.save with total.prepi PASSED ============================================================== 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 ============================================================== 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 leap && ./Run.tleap AMBERHOME is set to /home/msafi/amber11 Running leap tests on ./tleap -> ../../bin/teLeap building force field libraries: '91 ff.. diffing /home/msafi/amber11/dat/leap/lib/all_amino91.lib with all_amino91.lib PASSED ============================================================== diffing /home/msafi/amber11/dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib PASSED ============================================================== diffing /home/msafi/amber11/dat/leap/lib/all_aminont91.lib with all_aminont91.lib PASSED ============================================================== diffing /home/msafi/amber11/dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib PASSED ============================================================== diffing /home/msafi/amber11/dat/leap/lib/ions91.lib with ions91.lib PASSED ============================================================== '94 ff.. diffing /home/msafi/amber11/dat/leap/lib/all_amino94.lib with all_amino94.lib PASSED ============================================================== diffing /home/msafi/amber11/dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib PASSED ============================================================== diffing /home/msafi/amber11/dat/leap/lib/all_aminont94.lib with all_aminont94.lib PASSED ============================================================== diffing /home/msafi/amber11/dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib PASSED ============================================================== diffing /home/msafi/amber11/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 sleap && make -k test make[2]: Entering directory `/home/msafi/amber11/AmberTools/test/sleap' /bin/rm -f `find . -name "*.dif"` /bin/rm -f TEST_FAILURES.diff cd mdlsdf; ./Run.mdlsdf diffing crown_2.sdf.save with crown_2.sdf PASSED ============================================================== cd tripos; ./Run.tripos diffing wy.mol2.save with wy.mol2 PASSED ============================================================== cd pdbent; ./Run.pdbent1 diffing 1hpv.mol2.save with 1hpv.mol2 PASSED ============================================================== cd pdbent; ./Run.pdbent2 diffing mdl_1hpv.mol2.save with mdl_1hpv.mol2 PASSED ============================================================== cd offlib; ./Run.off diffing hpv.off.save with hpv.off PASSED ============================================================== cd source; ./Run.source diffing source.out.save with source.out PASSED ============================================================== cd prmtop; ./Run.prmtop1 diffing hpv.top.save with hpv.top PASSED ============================================================== diffing hpv.xyz.save with hpv.xyz PASSED ============================================================== cd prmtop; ./Run.prmtop2 This is a long test; please wait patiently... diffing box.out.save with box.out PASSED ============================================================== diffing hpv_box.top.save with hpvbox.top PASSED ============================================================== cd prmtop; ./Run.prmtop3 This is a long test; please wait patiently... diffing hpv_cap.top.save with hpv_cap.top PASSED ============================================================== cd prmtop; ./Run.prmtoppol diffing ubqpol.top.save with ubqpol.top PASSED ============================================================== diffing ubqpol.xyz.save with ubqpol.xyz PASSED ============================================================== cd solvate; ./Run.solvatebox This is a long test; please wait patiently... diffing hpvbox.pdb.save with hpvbox.pdb PASSED ============================================================== diffing hpvbox.top.save with hpvbox.top PASSED ============================================================== cd solvate; ./Run.solvatebox_closeness This is a long test; please wait patiently... diffing hpvbox_closeness.pdb.save with hpvbox_closeness.pdb PASSED ============================================================== cd solvate; ./Run.solvatecap diffing hpvcap.pdb.save with hpvcap.pdb PASSED ============================================================== cd solvate; ./Run.solvateoct This is a long test; please wait patiently... diffing hpvoct.pdb.save with hpvoct.pdb PASSED ============================================================== diffing hpvoct.top.save with hpvoct.top PASSED ============================================================== cd solvate; ./Run.solvateshell This is a long test; please wait patiently... diffing hpvshell.pdb.save with hpvshell.pdb PASSED ============================================================== cd amoeba; ./Run.amoeba diffing jac_2.prmtop.save with jac_2.prmtop PASSED ============================================================== cd amoeba; ./Run.amoeba_sol diffing hpv.prmtop.save with hpv.prmtop PASSED ============================================================== cd builder; ./Run.builder diffing water.mol2.save with water.mol2 PASSED ============================================================== diffing wat2.mol2.save with wat2.mol2 PASSED ============================================================== cd builder; ./Run.delete diffing ala_1.mol2.save with ala_1.mol2 PASSED ============================================================== diffing ala_2.mol2.save with ala_2.mol2 PASSED ============================================================== cd addions; ./Run.addions1 diffing hpv_ion.pdb.save with hpv_ion.pdb PASSED ============================================================== cd addions; ./Run.addions2 diffing hpv_ion2.pdb.save with hpv_ion2.pdb PASSED ============================================================== cd addions; ./Run.addions3 diffing 1zik_ion.mol2.save with 1zik_ion.mol2 PASSED ============================================================== cd molinfo; ./Run.molinfo diffing leap.out.save with leap.out PASSED ============================================================== cd polymer; ./Run.polymer diffing combine.mol2.save with combine.mol2 PASSED ============================================================== diffing sequence.mol2.save with sequence.mol2 PASSED ============================================================== cd polymer; ./Run.impose diffing impose.out.save with impose.out PASSED ============================================================== diffing impose.mol2.save with impose.mol2 PASSED ============================================================== cd polymer; ./Run.polymer2 diffing aa.mol2.save with aa.mol2 PASSED ============================================================== cd polymer; ./Run.zmatrix diffing zmatrix.out.save with zmatrix.out PASSED ============================================================== diffing meoh.mol2.save with meoh.mol2 PASSED ============================================================== cd bondbydis; ./Run.bondbydis diffing wy.sdf.save with wy.sdf PASSED ============================================================== cd DNA; ./Run.DNA1 diffing 132d.mol2.save with 132d.mol2 PASSED ============================================================== cd DNA; ./Run.DNA2 diffing 32d.top.save with 32d.top PASSED ============================================================== cd oldleap; ./Run.oldleap diffing ff91/all_amino91.lib.save with ff91/all_amino91.lib PASSED ============================================================== diffing ff91/all_aminont91.lib.save with ff91/all_aminont91.lib PASSED ============================================================== diffing ff91/all_aminoct91.lib.save with ff91/all_aminoct91.lib PASSED ============================================================== diffing ff91/all_nucleic91.lib.save with ff91/all_nucleic91.lib PASSED ============================================================== diffing ff94/all_amino94.lib.save with ff94/all_amino94.lib PASSED ============================================================== diffing ff94/all_aminont94.lib.save with ff94/all_aminont94.lib PASSED ============================================================== diffing ff94/all_aminoct94.lib.save with ff94/all_aminoct94.lib PASSED ============================================================== diffing ff94/all_nucleic94.lib.save with ff94/all_nucleic94.lib PASSED ============================================================== diffing ff94/all_aminoan94.top.save with ff94/all_aminoan94.top PASSED ============================================================== diffing ff94/all_aminoan94.crd.save with ff94/all_aminoan94.crd PASSED ============================================================== diffing ff94/all_aminonc94.top.save with ff94/all_aminonc94.top PASSED ============================================================== diffing ff94/all_aminonc94.crd.save with ff94/all_aminonc94.crd PASSED ============================================================== diffing ff94/all_dna94.top.save with ff94/all_dna94.top PASSED ============================================================== diffing ff94/all_dna94.crd.save with ff94/all_dna94.crd PASSED ============================================================== diffing ff94/all_rna94.top.save with ff94/all_rna94.top PASSED ============================================================== diffing ff94/all_rna94.crd.save with ff94/all_rna94.crd PASSED ============================================================== cd disulfide; ./Run.auto diffing crn.mol2.save with crn.mol2 PASSED ============================================================== cd disulfide; ./Run.manu diffing crn.mol2.save with crn.mol2 PASSED ============================================================== cd disulfide; ./Run.auto.H diffing crn.H.mol2.save with crn.H.mol2 PASSED ============================================================== diffing crn.top.save with crn.top PASSED ============================================================== diffing crn.xyz.save with crn.xyz PASSED ============================================================== cd propdiol; ./Run.test1 diffing mol.prmtop.save with mol.prmtop PASSED ============================================================== diffing test1.out.save with test1.out PASSED ============================================================== cd propdiol; ./Run.test2 diffing mol2.prmtop.save with mol2.prmtop PASSED ============================================================== diffing test2.out.save with test2.out PASSED ============================================================== cd glycam; ./Run.test1 diffing n.pdb.save with n.pdb PASSED ============================================================== cd transform; ./Run.translate diffing meoh_trans1.mol2.save with meoh_trans1.mol2 PASSED ============================================================== diffing meoh_trans2.mol2.save with meoh_trans2.mol2 PASSED ============================================================== cd 14scale; ./Run.14scale_test1 diffing nma1.prmtop.save with nma1.prmtop PASSED ============================================================== cd 14scale; ./Run.14scale_test2 diffing nma2.prmtop.save with nma2.prmtop PASSED ============================================================== ./cpTESTF.sh make[2]: Leaving directory `/home/msafi/amber11/AmberTools/test/sleap' 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_bcopt && ./Run.dmp.min bcoption=5 diffing bc5.mdout.dmp.min.save with bc5.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 PASSED ============================================================== cd 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 pbsa_tsr && ./Run.tsrb.min diffing mdout.tsrb.min.save with mdout.tsrb.min PASSED ============================================================== cd pbsa_radi && ./Run.ion.min diffing ./out.save/Li.out.save with Li.out PASSED ============================================================== diffing ./out.save/Na.out.save with Na.out PASSED ============================================================== diffing ./out.save/K.out.save with K.out PASSED ============================================================== diffing ./out.save/Rb.out.save with Rb.out PASSED ============================================================== diffing ./out.save/Cs.out.save with Cs.out PASSED ============================================================== diffing ./out.save/F.out.save with F.out PASSED ============================================================== diffing ./out.save/Cl.out.save with Cl.out PASSED ============================================================== diffing ./out.save/IM.out.save with IM.out PASSED ============================================================== diffing ./out.save/Br.out.save with Br.out PASSED ============================================================== diffing ./out.save/I.out.save with I.out PASSED ============================================================== diffing ./out.save/MG.out.save with MG.out PASSED ============================================================== diffing ./out.save/Ca.out.save with Ca.out PASSED ============================================================== diffing ./out.save/Zn.out.save with Zn.out PASSED ============================================================== diffing ./out.save/tp3.out.save with tp3.out PASSED ============================================================== diffing ./out.save/ile.out.save with ile.out PASSED ============================================================== diffing ./out.save/leu.out.save with leu.out PASSED ============================================================== diffing ./out.save/val.out.save with val.out PASSED ============================================================== diffing ./out.save/phe.out.save with phe.out PASSED ============================================================== diffing ./out.save/trp.out.save with trp.out PASSED ============================================================== diffing ./out.save/hid.out.save with hid.out PASSED ============================================================== diffing ./out.save/hie.out.save with hie.out PASSED ============================================================== diffing ./out.save/nhe.out.save with nhe.out PASSED ============================================================== diffing ./out.save/tyr.out.save with tyr.out PASSED ============================================================== diffing ./out.save/ser.out.save with ser.out PASSED ============================================================== diffing ./out.save/thr.out.save with thr.out PASSED ============================================================== diffing ./out.save/cys.out.save with cys.out PASSED ============================================================== diffing ./out.save/cyx.out.save with cyx.out PASSED ============================================================== diffing ./out.save/met.out.save with met.out PASSED ============================================================== diffing ./out.save/lyn.out.save with lyn.out PASSED ============================================================== diffing ./out.save/ash.out.save with ash.out PASSED ============================================================== diffing ./out.save/glh.out.save with glh.out PASSED ============================================================== diffing ./out.save/asn.out.save with asn.out PASSED ============================================================== diffing ./out.save/gln.out.save with gln.out PASSED ============================================================== diffing ./out.save/nma.out.save with nma.out PASSED ============================================================== diffing ./out.save/alabk.out.save with alabk.out PASSED ============================================================== diffing ./out.save/glybk.out.save with glybk.out PASSED ============================================================== diffing ./out.save/probk.out.save with probk.out PASSED ============================================================== diffing ./out.save/da.out.save with da.out PASSED ============================================================== diffing ./out.save/dc.out.save with dc.out PASSED ============================================================== diffing ./out.save/dg.out.save with dg.out PASSED ============================================================== diffing ./out.save/dt.out.save with dt.out PASSED ============================================================== diffing ./out.save/ru.out.save with ru.out PASSED ============================================================== diffing ./out.save/arg.out.save with arg.out PASSED ============================================================== diffing ./out.save/asp.out.save with asp.out PASSED ============================================================== diffing ./out.save/cym.out.save with cym.out PASSED ============================================================== diffing ./out.save/glu.out.save with glu.out PASSED ============================================================== diffing ./out.save/hip.out.save with hip.out PASSED ============================================================== diffing ./out.save/lys.out.save with lys.out PASSED ============================================================== diffing ./out.save/dap.out.save with dap.out PASSED ============================================================== diffing ./out.save/da3p.out.save with da3p.out PASSED ============================================================== diffing ./out.save/da5p.out.save with da5p.out PASSED ============================================================== diffing ./out.save/danp.out.save with danp.out PASSED ============================================================== diffing ./out.save/rap.out.save with rap.out PASSED ============================================================== diffing ./out.save/ra3p.out.save with ra3p.out PASSED ============================================================== diffing ./out.save/ra5p.out.save with ra5p.out PASSED ============================================================== diffing ./out.save/ranp.out.save with ranp.out PASSED ============================================================== cd pbsa_npb && ./test pbsa.ncg.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.ncg.bc6 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nsor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.nsor.bc6 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.asor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.asor.bc6 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.dsor.bc5 diffing mdout.110D.min.save with mdout.110D.min PASSED ============================================================== pbsa.dsor.bc6 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.argasp checking argasp force PASSED ============================================================== dbf_0.dadt checking dadt force PASSED ============================================================== dbf_0.dgdc checking dgdc force PASSED ============================================================== dbf_0.lysasp checking lysasp force PASSED ============================================================== dbf_0.polyALA checking polyALA force PASSED ============================================================== dbf_0.polyAT checking polyAT force PASSED ============================================================== dbf_1.argasp checking argasp force PASSED ============================================================== dbf_1.dadt checking dadt force PASSED ============================================================== dbf_1.dgdc checking dgdc force PASSED ============================================================== dbf_1.lysasp checking lysasp force PASSED ============================================================== dbf_1.polyALA checking polyALA force PASSED ============================================================== dbf_1.polyAT checking polyAT force PASSED ============================================================== dbf_2.argasp checking argasp force PASSED ============================================================== dbf_2.dadt checking dadt force PASSED ============================================================== dbf_2.dgdc checking dgdc force PASSED ============================================================== dbf_2.lysasp checking lysasp force PASSED ============================================================== dbf_2.polyALA checking polyALA force PASSED ============================================================== dbf_2.polyAT checking polyAT force PASSED ============================================================== dbf_3.argasp checking argasp force PASSED ============================================================== dbf_3.dadt checking dadt force PASSED ============================================================== dbf_3.dgdc checking dgdc force diffing force.save with force.dat PASSED ============================================================== ============================================================== dbf_3.lysasp checking lysasp force diffing force.save with force.dat PASSED ============================================================== ============================================================== dbf_3.polyALA checking polyALA force 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 && ./Run.1az6.min diffing mdout.1az6.min.save with mdout.1az6.min PASSED ============================================================== cd pbsa_IIM && ./Run.IIM.min diffing mdout.min_bc6_solv1.save with mdout.min_bc6_solv1 PASSED ============================================================== 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 mmpbsa_py && make test make[2]: Entering directory `/home/msafi/amber11/AmberTools/test/mmpbsa_py' cd 01_Generalized_Born && ./Run.GB diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== cd 02_Poisson_Boltzmann && ./Run.PB diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== cd 03_Alanine_Scanning && ./Run.ALA diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing orig_mutant.mdcrd with _MMPBSA_mutant_complex.mdcrd PASSED ============================================================== cd 04_Per_Residue_Decomp && ./Run.PerRes diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat PASSED ============================================================== cd 05_Pairwise_Decomp && ./Run.Pairwise diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat PASSED ============================================================== cd 06_NAB_Nmode && ./Run.nmode diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif ============================================================== cd 07_Comprehensive && ./Run.comprehensive diffing FINAL_RESULTS_MMPBSA_1.dat.save with FINAL_RESULTS_MMPBSA_1.dat PASSED ============================================================== diffing FINAL_RESULTS_MMPBSA_2.dat.save with FINAL_RESULTS_MMPBSA_2.dat PASSED ============================================================== diffing FINAL_DECOMP_MMPBSA.dat.save with FINAL_DECOMP_MMPBSA.dat PASSED ============================================================== diffing FINAL_DECOMP_MMPBSA_2.dat.save with FINAL_DECOMP_MMPBSA_2.dat PASSED ============================================================== cd 08_Stability && ./Run.stability diffing FINAL_RESULTS_MMPBSA1.dat.save with FINAL_RESULTS_MMPBSA1.dat PASSED ============================================================== diffing FINAL_DECOMP_MMPBSA1.dat.save with FINAL_DECOMP_MMPBSA1.dat PASSED ============================================================== diffing FINAL_RESULTS_MMPBSA2.dat.save with FINAL_RESULTS_MMPBSA2.dat possible FAILURE: check FINAL_RESULTS_MMPBSA2.dat.dif ============================================================== diffing FINAL_DECOMP_MMPBSA2.dat.save with FINAL_DECOMP_MMPBSA2.dat possible FAILURE: check FINAL_DECOMP_MMPBSA2.dat.dif ============================================================== cd 09_APBS_Poisson_Boltzmann && ./Run.PB This is a test for sander.APBS, but sander.APBS cannot be found. Install sander.APBS in order to run this test. cd 10_QM_MMGBSA && ./Run.QMMMGBSA diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== cd 11_3D-RISM && ./Run.rism3d diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== Reading command-line arguments and input files... Cleaning temporary files make[2]: Leaving directory `/home/msafi/amber11/AmberTools/test/mmpbsa_py' cd ambpdb && ./Run.ambpdb | New format PARM file being parsed. | Version = 1.000 Date = 02/19/04 Time = 15:33:29 | New format PARM file being parsed. | Version = 1.000 Date = 02/19/04 Time = 15:33:29 | New format PARM file being parsed. | Version = 1.000 Date = 02/19/04 Time = 15:33:29 diffing restrt.pdb.save with restrt.pdb PASSED ============================================================== diffing restrt.mol2.save with restrt.mol2 PASSED ============================================================== diffing restrt.pqr.save with restrt.pqr PASSED ============================================================== cd ambpdb_first_protein && ./Run.ambpdb | New format PARM file being parsed. | Version = 1.000 Date = 02/15/07 Time = 16:57:28 diffing first.pdb.save with first.pdb PASSED ============================================================== cd ambpdb_first_rna && ./Run.ambpdb | New format PARM file being parsed. | Version = 1.000 Date = 05/18/06 Time = 18:52:52 diffing first.pdb.save with first.pdb PASSED ============================================================== cd elsize && ./Run.elsize diffing elsize_out.trxox.save with elsize_out.trxox PASSED ============================================================== cd ./chamber/trans-but-2-ene && ./Run /bin/rm: No match. diffing chamber.out.save with chamber.out PASSED ============================================================== diffing prmtop.save with prmtop PASSED ============================================================== diffing inpcrd.save with inpcrd PASSED ============================================================== cd ./chamber/ala_ala_ala && ./Run /bin/rm: No match. diffing chamber.out.save with chamber.out PASSED ============================================================== diffing prmtop.save with prmtop PASSED ============================================================== diffing inpcrd.save with inpcrd PASSED ============================================================== cd ./chamber/poly_pro_gas && ./Run.poly_pro_gas_chamber diffing chamber.crd.out.save with chamber.crd.out PASSED ============================================================== diffing poly_pro_gas_all22.crd.prmtop.save with poly_pro_gas_all22.crd.prmtop PASSED ============================================================== diffing poly_pro_gas_all22.crd.inpcrd.save with poly_pro_gas_all22.crd.inpcrd PASSED ============================================================== diffing chamber.pdb.out.save with chamber.pdb.out PASSED ============================================================== diffing poly_pro_gas_all22.pdb.prmtop.save with poly_pro_gas_all22.pdb.prmtop PASSED ============================================================== diffing poly_pro_gas_all22.pdb.inpcrd.save with poly_pro_gas_all22.pdb.inpcrd PASSED ============================================================== cd ./chamber/glucose && ./Run /bin/rm: No match. diffing chamber.out.save with chamber.out PASSED ============================================================== diffing prmtop.save with prmtop PASSED ============================================================== diffing inpcrd.save with inpcrd PASSED ============================================================== cd ./chamber/dhfr_gas && ./Run.dhfr_gas_chamber diffing chamber.out.save with chamber.out PASSED ============================================================== diffing dhfr_gas_all22_prot.prmtop.save with dhfr_gas_all22_prot.prmtop PASSED ============================================================== diffing dhfr_gas_all22_prot.inpcrd.save with dhfr_gas_all22_prot.inpcrd PASSED ============================================================== cd ./chamber/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_chamber /bin/rm: No match. diffing chamber.out.save with chamber.out PASSED ============================================================== diffing prmtop.save with prmtop PASSED ============================================================== diffing inpcrd.save with inpcrd 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 ============================================================== if [ -n "rism" ]; then cd ./rism1d/spc-kh && ./Run.spc; fi diffing spc.xvv.delhv0.save with spc.xvv.delhv0 PASSED ============================================================== diffing spc.xvv.xvv.save with spc.xvv.xvv 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.td.save with spc.td 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 "rism" ]; 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.xvv.save with spc-nacl-3.xvv.xvv 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.cvv.save with spc-nacl-3.cvv PASSED ============================================================== diffing spc-nacl-3.td.save with spc-nacl-3.td 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.svv.save with spc-nacl-3.svv PASSED ============================================================== if [ -n "rism" ]; 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.xvv.save with spc-lj.xvv.xvv 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.td.save with spc-lj.td 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 "rism" ]; then cd ./rism1d/spc-mv0 && ./Run.spc; fi diffing spc.xvv.delhv0.save with spc.xvv.delhv0 PASSED ============================================================== diffing spc.xvv.xvv.save with spc.xvv.xvv 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.td.save with spc.td 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 "rism" ]; then cd ./rism1d/lj-py && ./Run.lj; fi diffing lj.xvv.delhv0.save with lj.xvv.delhv0 PASSED ============================================================== diffing lj.xvv.xvv.save with lj.xvv.xvv 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.td.save with lj.td 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 "rism" ]; then cd ./rism1d/tip3p-kh && ./Run.tip3p; fi diffing tip3p.xvv.delhv0.save with tip3p.xvv.delhv0 PASSED ============================================================== diffing tip3p.xvv.xvv.save with tip3p.xvv.xvv 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.td.save with tip3p.td 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 ============================================================== Finished test suite for AmberTools at Wed Jun 22 14:58:32 EDT 2011. make[1]: Leaving directory `/home/msafi/amber11/AmberTools/test' 508 file comparisons passed 3 file comparisons failed 0 tests experienced errors