./test_at_clean.sh cd mmpbsa_py && make -k clean cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 02_Poisson_Boltzmann && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 03_Alanine_Scanning && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 04_Per_Residue_Decomp && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 05_Pairwise_Decomp && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 06_NAB_Nmode && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 07_Comprehensive && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 08_Stability && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 09_APBS_Poisson_Boltzmann && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 10_QM_MMGBSA && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd 11_3D-RISM && /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA -clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif /bin/sh: /Users/jennifer.muzyka/opt/amber11/bin/MMPBSA: No such file or directory make[2]: [clean] Error 127 (ignored) cd cpptraj && make -k clean 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 bench.all OPT=clean cd nab && make -k testrism Running test to make dna duplex: ./Run.duplex: line 10: ../../bin/nab: No such file or directory ./Run.duplex: Program error make[2]: *** [duplex_test] Error 1 Running test to computed 3DNA deformation energies: ./Run.deform: line 11: ../../bin/nab: No such file or directory ./Run.deform: Program error make[2]: *** [deform_test] Error 1 Running Reflexive test: ./Run.reflexive: line 11: ../../bin/nab: No such file or directory ./Run.reflexive: Program error make[2]: *** [reflexive_test] Error 1 Running test of hashed arrays: ./Run.hashed: line 11: ../../bin/nab: No such file or directory ./Run.hashed: Program error make[2]: *** [hashed_test] Error 1 Running test to compute chemical shifts (this tests many parts of the compiler and libraries) ./Run.shifts: line 12: ../../bin/nab: No such file or directory ./Run.shifts: Program error make[2]: *** [shifts_test] Error 1 Running test to do simple minimization (this tests the molecular mechanics interface) ./Run.sff: line 14: ../../bin/nab: No such file or directory ./Run.sff: Program error make[2]: *** [sff_test] Error 1 Running test to do simple minimization with shake (this tests the molecular mechanics interface) ./Run.shake: line 14: ../../bin/nab: No such file or directory ./Run.shake: Program error make[2]: *** [rattle_min_test] Error 1 Running test of fibre-diffraction module ./Run.fd: line 13: ../../bin/nab: No such file or directory ./Run.fd: Program error make[2]: *** [fd_test] Error 1 Running test to do simple minimization (this tests the generalized Born implementation) ./Run.gb: line 14: ../../bin/nab: No such file or directory ./Run.gb: Program error make[2]: *** [gb_test] Error 1 Running test to do simple minimization (this tests the generalized Born implementation) ./Run.xfin: line 14: ../../bin/nab: No such file or directory ./Run.xfin: Program error make[2]: *** [xfin_test] Error 1 Running test to do simple minimization (this tests the LCPO surface area) ./Run.gbsa: line 14: ../../bin/nab: No such file or directory ./Run.gbsa: Program error make[2]: *** [gbsa_test] Error 1 Running test to do simple minimization (this tests the ao generalized Born implementation) ./Run.gb2: line 14: ../../bin/nab: No such file or directory ./Run.gb2: Program error make[2]: *** [gb2_test] Error 1 Running test to do molecular dynamics with rattle ./Run.rattle_md: line 13: ../../bin/nab: No such file or directory ./Run.rattle_md: Program error make[2]: *** [rattle_md_test] Error 1 Running test of randomized embedding ./Run.rembed: line 11: ../../bin/nab: No such file or directory ./Run.rembed: Program error make[2]: *** [rembed_test] Error 1 Running test to compute NAB energy of 3dfr minus waters. ./Run.dhfrndpmtx: line 13: ../../bin/nab: No such file or directory ./Run.dhfrndpmtx: Program error make[2]: *** [dhfrndpmtx_test] Error 1 Running test to compute GB Newton-Raphson and normal modes: ./Run.asp: line 13: ../../bin/nab: No such file or directory ./Run.asp: Program error make[2]: *** [asp_test] Error 1 Running test to compute non-GB Newton-Raphson and normal modes: ./Run.aspnb: line 13: ../../bin/nab: No such file or directory ./Run.aspnb: Program error make[2]: *** [aspnb_test] Error 1 Running test to create Amber force-field description ./Run.prm: line 13: ../../bin/nab: No such file or directory ./Run.prm: Program error make[2]: *** [prm_test] Error 1 Running test to create a simple mmCIF file ./Run.cif: line 11: ../../bin/nab: No such file or directory ./Run.cif: Program error make[2]: *** [cif_test] Error 1 Running test to do simple xmin minimization ./Run.xmin: line 13: ../../bin/nab: No such file or directory ./Run.xmin: Program error make[2]: *** [xmin_test] Error 1 Running test on netcdf files ./Run.netcdf: line 13: ../../bin/nab: No such file or directory ./Run.netcdf: Program error make[2]: *** [netcdf_test] Error 1 Running test to do simple lmod optimization ./Run.lmod: line 13: ../../bin/nab: No such file or directory ./Run.lmod: Program error make[2]: *** [lmod_test] Error 1 Running test to compute GB normal modes using DSYEVD: ./Run.nmode1: line 13: ../../bin/nab: No such file or directory ./Run.nmode1: Program error make[2]: *** [nmode1_test] Error 1 Running test to compute GB normal modes using DSAUPD: ./Run.nmode2: line 13: ../../bin/nab: No such file or directory ./Run.nmode2: Program error make[2]: *** [nmode2_test] Error 1 Running test to compute Langevin modes: ./Run.nmode3: line 13: ../../bin/nab: No such file or directory ./Run.nmode3: Program error make[2]: *** [nmode3_test] Error 1 Running test of the isotropic periodic sum technique ./Run.ips: line 13: ../../bin/nab: No such file or directory ./Run.ips: Program error make[2]: *** [ips_test] Error 1 Running test to do simple minimization (libpbsa) (this tests the PBSA implementation) ./Run.pbsa: line 14: ../../bin/nab: No such file or directory ./Run.pbsa: Program error make[2]: *** [pbsa_test] Error 1 Running test to do simple minimization (librism) (this tests the 3D-RISM implementation) ./Run.rism_min: line 40: ../../bin/nab: No such file or directory ./Run.rism_min: Program error make[2]: *** [rism_test] Error 1 Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) ./Run.rism_md: line 39: ../../bin/nab: No such file or directory ./Run.rism_md: Program error make[2]: *** [rism_md_test] Error 1 Running test to do basic MD (librism) (this tests the 3D-RISM-KH precission) ./Run.rism_dist: line 33: ../../bin/nab: No such file or directory ./Run.rism_dist: Program error make[2]: *** [rism_dist] Error 1 Running test to do basic MD (librism) (this tests the 3D-RISM-HNC implementation) ./Run.rism_hnc: line 37: ../../bin/nab: No such file or directory ./Run.rism_hnc: Program error make[2]: *** [rism_hnc] Error 1 Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) ./Run.rism_ion: line 39: ../../bin/nab: No such file or directory ./Run.rism_ion: Program error make[2]: *** [rism_ion] Error 1 Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) ./Run.rism_md_nocut: line 39: ../../bin/nab: No such file or directory ./Run.rism_md_nocut: Program error make[2]: *** [rism_nocut] Error 1 Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) ./Run.rism_md_pse1: line 39: ../../bin/nab: No such file or directory ./Run.rism_md_pse1: Program error make[2]: *** [rism_md_pse1] Error 1 Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) ./Run.rism_ion-noasymp: line 39: ../../bin/nab: No such file or directory ./Run.rism_ion-noasymp: Program error make[2]: *** [rism_ion-noasymp] Error 1 Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) ./Run.rism_ion_pse1: line 39: ../../bin/nab: No such file or directory ./Run.rism_ion_pse1: Program error make[2]: *** [rism_ion_pse1] Error 1 Running test for ionic solvent and charge solute (this tests the 3D-RISM-KH implementation) ./Run.rism_ion_pse3: line 39: ../../bin/nab: No such file or directory ./Run.rism_ion_pse3: Program error make[2]: *** [rism_ion_pse3] Error 1 Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) ./Run.rism_mdiis0: line 39: ../../bin/nab: No such file or directory ./Run.rism_mdiis0: Program error make[2]: *** [rism_mdiis0] Error 1 Running test to do basic MD (librism) (this tests the 3D-RISM-KH implementation) ./Run.rism_mdiis1: line 39: ../../bin/nab: No such file or directory ./Run.rism_mdiis1: Program error make[2]: *** [rism_mdiis1] Error 1 Running test to do basic MD (librism) (trajectory processing using the 3D-RISM command line interface) ./Run.rism_sp: line 43: /Users/jennifer.muzyka/opt/amber11/bin/rism3d.snglpnt: No such file or directory ./Run.rism_sp: Program error make[2]: *** [rism_sp] Error 1 Running test to do basic MD (librism) (trajectory processing version 2 using the 3D-RISM command line interface) ./Run.rism_sp2: line 36: /Users/jennifer.muzyka/opt/amber11/bin/rism3d.snglpnt: No such file or directory ./Run.rism_sp2: Program error make[2]: *** [rism_sp2] Error 1 make[2]: Target `testrism' not remade because of errors. make[1]: *** [test.nab] Error 2 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 test.all CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.general] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.strip] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.strip] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.brokentraj] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.traj] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.remdnetcdf] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.framerange] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.perres] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.dssp] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.hbond] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.ptrajcomp] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.surf] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.radgyr] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.mask] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.rmsd] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.mol2] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.nastruct] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.pucker] Error 1 (ignored) CPPTRAJ not found (/Users/jennifer.muzyka/opt/amber11/bin/cpptraj). make[3]: [test.closest] Error 1 (ignored) 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 ../../../bin/tleap: Command not found. diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out possible FAILURE: check leap.out.dif ============================================================== 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 /Users/jennifer.muzyka/opt/amber11 Error: ./tleap -> ../../bin/teLeap does not exist make[1]: *** [test.leap] Error 1 cd sleap && make -k test /bin/rm -f `find . -name "*.dif"` /bin/rm -f TEST_FAILURES.diff make[2]: *** No rule to make target `../../bin/sleap', needed by `test'. make[2]: Target `test' not remade because of errors. make[1]: *** [test.sleap] Error 2 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 cd 01_Generalized_Born && ./Run.GB ./Run.GB: Program error make[2]: *** [GB] Error 1 cd 02_Poisson_Boltzmann && ./Run.PB ./Run.PB: Program error make[2]: *** [PB] Error 1 cd 03_Alanine_Scanning && ./Run.ALA ./Run.ALA: Program error make[2]: *** [ALA] Error 1 cd 04_Per_Residue_Decomp && ./Run.PerRes This test requires sander and can only be run with Amber11 installed. cd 05_Pairwise_Decomp && ./Run.Pairwise This test requires sander and can only be run with Amber11 installed. cd 06_NAB_Nmode && ./Run.nmode ./Run.nmode: Program error make[2]: *** [NAB] Error 1 cd 07_Comprehensive && ./Run.comprehensive This test requires sander and can only be run with Amber11 installed. cd 08_Stability && ./Run.stability This test requires sander and can only be run with Amber11 installed. 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 This test requires sander and can only be run with Amber11 installed. cd 11_3D-RISM && ./Run.rism3d ./Run.rism3d: Program error make[2]: *** [3DRISM] Error 1 make[2]: Target `test' not remade because of errors. make[1]: *** [test.mmpbsa] Error 2 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 ../../../bin/rism1d: Command not found. ./Run.spc: Program error make[1]: [test.rism1d] Error 1 (ignored) if [ -n "rism" ]; then cd ./rism1d/spc-psen && ./Run.spc-nacl-3; fi ../../../bin/rism1d: Command not found. ./Run.spc-nacl-3: Program error make[1]: [test.rism1d] Error 1 (ignored) if [ -n "rism" ]; then cd ./rism1d/spc-hnc && ./Run.spc-lj; fi ../../../bin/rism1d: Command not found. ./Run.spc-lj: Program error make[1]: [test.rism1d] Error 1 (ignored) if [ -n "rism" ]; then cd ./rism1d/spc-mv0 && ./Run.spc; fi ../../../bin/rism1d: Command not found. ./Run.spc: Program error make[1]: [test.rism1d] Error 1 (ignored) if [ -n "rism" ]; then cd ./rism1d/lj-py && ./Run.lj; fi ../../../bin/rism1d: Command not found. ./Run.lj: Program error make[1]: [test.rism1d] Error 1 (ignored) if [ -n "rism" ]; then cd ./rism1d/tip3p-kh && ./Run.tip3p; fi ../../../bin/rism1d: Command not found. ./Run.tip3p: Program error make[1]: [test.rism1d] Error 1 (ignored) Finished test suite for AmberTools at Wed Jul 6 08:02:51 EDT 2011. make[1]: Target `test.serial' not remade because of errors. 216 file comparisons passed 1 file comparison failed 143 tests experienced errors