make[2]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test' ./test_at_clean.sh cd mmpbsa_py && make -k clean make[3]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/mmpbsa_py' cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 02_Poisson_Boltzmann && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 03_Alanine_Scanning && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 04_Per_Residue_Decomp && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 05_Pairwise_Decomp && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 06_NAB_Nmode && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 07_Comprehensive && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 08_Stability && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 09_APBS_Poisson_Boltzmann && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 10_QM_MMGBSA && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 11_3D-RISM && /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/MMPBSA.py --clean > /dev/null && /bin/rm -f mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv make[3]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/mmpbsa_py' cd cpptraj && make -k clean make[3]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' Cleaning all test directories: (find . -name 'test.out' -o -name 'valgrind.out' -o -name 'Thread.*' \ -o -name 'Test_Results.dat' -o -name 'Test_Error.dat' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) make test.complete OPT=clean make[4]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' make[4]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' make[3]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' cd leap/glycam && ./Run_tests.bash clean cd nab && make -k test make[3]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/nab' Running test to make dna duplex: diffing d01.pdb.check with d01.pdb PASSED ============================================================== Running test to computed 3DNA deformation energies: diffing deform.out.check with deform.out PASSED ============================================================== Running Reflexive test: diffing ref.out.check with ref.out PASSED ============================================================== Running test of sub() and gsub() diffing gsub_test.out.check with gsub_test.out PASSED ============================================================== Running test of hashed arrays: diffing hash.out.check with hash.out PASSED ============================================================== Running test to compute chemical shifts (this tests many parts of the compiler and libraries) diffing 5pti.shifts.check with 5pti.shifts PASSED ============================================================== Running test to do simple minimization (this tests the molecular mechanics interface) diffing ltest.out.check with ltest.out PASSED ============================================================== Running test to do simple minimization with shake (this tests the molecular mechanics interface) diffing rattle_min.out.check with rattle_min.out PASSED ============================================================== Running test of fibre-diffraction module diffing fd.pdb.check with fd.pdb PASSED ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing gbrna.out.check with gbrna.out PASSED ============================================================== Running test to do simple minimization (this tests the generalized Born implementation) diffing xfin_sa.out.check with xfin_sa.out PASSED ============================================================== Running test to do simple minimization (this tests the LCPO surface area) diffing gbrna_sa.out.check with gbrna_sa.out PASSED ============================================================== Running test to do simple minimization (this tests the ao generalized Born implementation) diffing gbtrx.out.check with gbtrx.out PASSED ============================================================== Running test to do molecular dynamics with rattle diffing rattle_md.out.check with rattle_md.out PASSED ============================================================== Running test of randomized embedding diffing rembed.out.check with rembed.out PASSED ============================================================== Running test to compute NAB energy of 3dfr minus waters. Compare the NAB energy with the previously computed Amber energy: Amber8 total energy is 5184.0880 NAB total energy is 5184.0880 diffing dhfrndpmtx.out.check with dhfrndpmtx.out PASSED ============================================================== Running test to compute GB Newton-Raphson and normal modes: Note: Very small differences between asp.out and the saved file are common and do not necessarily indicate a problem. diffing asp.out.check with asp.out PASSED ============================================================== Running test to compute non-GB Newton-Raphson and normal modes: Note: Small differences are common and do not necessarily indicate a problem. diffing aspnb.out.check with aspnb.out PASSED ============================================================== Running test to create Amber force-field description diffing prm.out.check with prm.out PASSED ============================================================== checking the prmtop file: diffing tprmtop.check with tprmtop PASSED ============================================================== Running test to create a simple mmCIF file 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 ============================================================== make[3]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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 /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/include/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 /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/include/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[3]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' make test.all make[4]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_General CPPTRAJ: General tests diffing distance.dat.save with distance.dat PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing rmsda.dat.save with rmsda.dat PASSED ============================================================== diffing phi2.dat.save with phi2.dat PASSED ============================================================== diffing PhiPsi.dat.save with PhiPsi.dat PASSED ============================================================== diffing test.crd.save with test.crd PASSED ============================================================== diffing a1.dat.save with a1.dat PASSED ============================================================== diffing test.rst7.213.save with Restart/test.rst7.213 PASSED ============================================================== diffing 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: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Strip CPPTRAJ: One frame strip command test. diffing dummy.pdb.save with dummy.pdb PASSED ============================================================== diffing dummy.rst7.save with dummy.rst7 PASSED ============================================================== diffing strip.tz2.truncoct.parm7.save with strip.tz2.truncoct.parm7 PASSED ============================================================== CPPTRAJ: Unstrip (Lig/Rec/Complex) command test. diffing strip.tz2.truncoct.parm7.save with complex.tz2.truncoct.parm7 PASSED ============================================================== diffing receptor.tz2.truncoct.parm7.save with receptor.tz2.truncoct.parm7 PASSED ============================================================== diffing ligand.tz2.truncoct.parm7.save with ligand.tz2.truncoct.parm7 PASSED ============================================================== diffing Ligand.crd.save with Ligand.crd PASSED ============================================================== diffing Receptor.crd.save with Receptor.crd PASSED ============================================================== diffing Complex.crd.save with Complex.crd PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Broken Traj: Running broken trajectory. diffing goodrmsd.dat with badrmsd.dat PASSED ============================================================== CPPTRAJ: Broken Traj: Running compressed broken trajectory. diffing goodrmsd.dat with ziprmsd.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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 ============================================================== CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: CRD Replica Trajectory Run with remdout diffing d1.crd.dat.save with d1.crd.dat PASSED ============================================================== diffing temp0.crd.300.00 with temp.crd.300.00 PASSED ============================================================== diffing temp0.crd.384.30 with temp.crd.384.30 PASSED ============================================================== diffing temp0.crd.492.20 with temp.crd.492.20 PASSED ============================================================== diffing temp0.crd.630.50 with temp.crd.630.50 PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] diffing test.rst7.3.save with test.rst7.3 PASSED ============================================================== diffing test.rst7.5.save with test.rst7.5 PASSED ============================================================== diffing test.rst7.6.save with test.rst7.6 PASSED ============================================================== diffing test.rst7.7.save with test.rst7.7 PASSED ============================================================== diffing test.rst7.8.save with test.rst7.8 PASSED ============================================================== CPPTRAJ: Trajout Frame Range [Amber Coordinates] diffing framerange.crd.save with framerange.crd PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. diffing PerResRMSD.agr.save with PerResRMSD.agr PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with averaging. diffing perresavg.dat.save with perresavg.dat PASSED ============================================================== CPPTRAJ: Per-Residue RMSD Test with residue centering. diffing center.agr.save with center.agr PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. diffing dssp.gnu.save with dssp.gnu PASSED ============================================================== diffing dssp.sum.agr.save with dssp.sum.agr PASSED ============================================================== CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. diffing dssp.dat.save with dssp.dat PASSED ============================================================== diffing dssp.dat.sum.save with dssp.dat.sum PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: NetCDF Restart Test - NetCDF->TXT diffing ../tz2.rst7 with text.rst7 PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Image CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: Non-orthorhombic imaged distance test. diffing ortho.dat.save with ortho.dat PASSED ============================================================== diffing nonortho.dat.save with nonortho.dat PASSED ============================================================== CPPTRAJ: Orthorhombic coordinate imaging test. CPPTRAJ: Nonorthorhombic coordinate imaging test. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM. diffing image.crd.save with image.crd PASSED ============================================================== diffing image2.crd.save with image2.crd PASSED ============================================================== diffing image3.crd.save with image3.crd PASSED ============================================================== diffing image4.crd.save with image4.crd PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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 ============================================================== diffing watershell.list.save with watershell.list PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Surf CPPTRAJ: Surface calculation test. diffing surf.dat.save with surf.dat PASSED ============================================================== CPPTRAJ: Partial Surface calculation test. diffing tsurf.dat.save with tsurf.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Mask CPPTRAJ: Mask command test. diffing mask.out.save with mask.out PASSED ============================================================== diffing mask.pdb.1.save with mask.pdb.1 PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing T1.crd with T2.crd PASSED ============================================================== diffing ../tz2.truncoct.crd with test.crd PASSED ============================================================== CPPTRAJ: Outtraj Test with maxmin option. diffing maxmin.crd.save with maxmin.crd PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Charmm CPPTRAJ: CHARMM PSF/DCD test diffing test.ala3.pdb.save with test.ala3.pdb PASSED ============================================================== CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: CHARMM DCD Write, step 2. diffing first.ala3.crd with second.ala3.crd PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Rotdif CPPTRAJ: Rotdif test diffing rvecs.dat.save with rvecs.dat PASSED ============================================================== diffing matrices.dat.save with matrices.dat PASSED ============================================================== diffing deffs.dat.save with deffs.dat PASSED ============================================================== diffing rotdif.out.save with rotdif.out PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Runavg CPPTRAJ: Coordinate Running Average diffing runavg.crd.save with runavg.crd PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr diffing rmscorr.dat.save with rmscorr.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_2DRMS CPPTRAJ: 2D RMSD Test. diffing rmsd.dat.save with rmsd2.dat PASSED ============================================================== CPPTRAJ: 2D RMSD Test, mass-weighted. diffing rmsd.mass.dat.save with rmsd.mass.dat PASSED ============================================================== CPPTRAJ: Generating ref traj for 2D RMSD test. CPPTRAJ: 2D RMSD Test with reference trajectory. diffing rmsd.dat.save with rmsd1.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. diffing L01.mol2.1.save with L01.mol2 PASSED ============================================================== diffing tz2.mol2.1.save with tz2.mol2 PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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 ============================================================== diffing Helix.nastruct.dat.save with Helix.nastruct.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Average CPPTRAJ: Average Test. diffing test.pdb.save with test.pdb PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/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: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_AtomMap CPPTRAJ: AtomMap Test diffing initial.mol2.save with initial.mol2 PASSED ============================================================== diffing atommap.dat.save with atommap.dat PASSED ============================================================== diffing reordered.pdb.save with reordered.pdb PASSED ============================================================== diffing reordered.mol2.save with reordered.mol2 PASSED ============================================================== diffing rmsd.dat.save with rmsd.dat PASSED ============================================================== diffing fit.mol2.save with fit.mol2 PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Datafile CPPTRAJ: Data file output precision test. diffing prec.dat.save with prec.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Radial CPPTRAJ: Radial Test diffing Radial.agr.save with Radial.agr PASSED ============================================================== diffing cRadial.agr.save with cRadial.agr PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Hist CPPTRAJ: Histogram Analysis Test diffing hist.gnu.save with hist.gnu PASSED ============================================================== diffing hist.agr.save with hist.agr PASSED ============================================================== diffing freeE.gnu.save with freeE.gnu PASSED ============================================================== diffing norm.gnu.save with norm.gnu PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Closest CPPTRAJ: Closest command test using first solvent atom. diffing first.Closest.pdb.save with first.Closest.pdb PASSED ============================================================== diffing closestmols.dat.save with closestmols.dat PASSED ============================================================== diffing closest.tz2.truncoct.parm7.save with closest.tz2.truncoct.parm7 PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_DRMSD CPPTRAJ: Distance RMSD test. diffing drmsd.dat.save with drmsd.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_Cluster CPPTRAJ: Cluster command test. diffing cnumvtime.dat.save with cnumvtime.dat PASSED ============================================================== diffing avg.summary.dat.save with avg.summary.dat PASSED ============================================================== diffing summary.dat.save with summary.dat PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_ptraj_action Comparing to ptraj: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/ptraj CPPTRAJ: atomicfluct test. diffing ptraj.fluct.dat with fluct.dat PASSED ============================================================== CPPTRAJ: clusterdihedral test. diffing ptraj.cd.dat with cd.dat PASSED ============================================================== diffing ptraj.cf.dat with cf.dat PASSED ============================================================== diffing ptraj.ci.dat with ci.dat PASSED ============================================================== CPPTRAJ: contacts test. diffing ptraj.contacts.dat with contacts.dat PASSED ============================================================== CPPTRAJ: diffusion test. diffing ptraj.diff_a.xmgr with diff_a.xmgr PASSED ============================================================== diffing ptraj.diff_r.xmgr with diff_r.xmgr PASSED ============================================================== diffing ptraj.diff_x.xmgr with diff_x.xmgr PASSED ============================================================== diffing ptraj.diff_y.xmgr with diff_y.xmgr PASSED ============================================================== diffing ptraj.diff_z.xmgr with diff_z.xmgr PASSED ============================================================== CPPTRAJ: grid test. diffing ptraj.test.crd with test.crd PASSED ============================================================== diffing ptraj.out.grid with out.grid PASSED ============================================================== CPPTRAJ: dipole test diffing ptraj.out.dipole with out.dipole PASSED ============================================================== CPPTRAJ: principal test. diffing ptraj.principal.crd with principal.crd PASSED ============================================================== CPPTRAJ: unwrap test diffing ptraj.unwrap.crd with unwrap.crd PASSED ============================================================== CPPTRAJ: randomizeions test diffing ptraj.random.crd with random.crd PASSED ============================================================== ************************************************************** TEST: /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj/Test_CheckStructure CPPTRAJ: Structure Check diffing report.dat.save with report.dat PASSED ============================================================== make[4]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' make[3]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/cpptraj' cd antechamber/bondtype && ./Run.bondtype diffing ABAKOE.prepi.save with ABAKOE.prepi PASSED ============================================================== diffing PFPHHG02.prepi.save with PFPHHG02.prepi PASSED ============================================================== diffing fluorescein2.mol2.save with fluorescein2.mol2 PASSED ============================================================== diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2 PASSED ============================================================== cd antechamber/c60 && ./Run.c60 diffing buckyball.mol2.save with buckyball.mol2 PASSED ============================================================== diffing buckyball.gzmat.save with buckyball.gzmat PASSED ============================================================== diffing buckyball.jcrt.save with buckyball.jcrt PASSED ============================================================== diffing buckyball.prepi.save with buckyball.prepi PASSED ============================================================== diffing buckyball.ac.save with buckyball.ac PASSED ============================================================== cd antechamber/charmm && ./Run.charmm diffing ala2.inp.save with ala2.inp PASSED ============================================================== diffing ala2.rtf.save with ala2.rtf PASSED ============================================================== diffing ala2.prm.save with ala2.prm PASSED ============================================================== diffing ala2_charmm.mol2.save with ala2_charmm.mol2 PASSED ============================================================== cd antechamber/chemokine && ./Run.1b2t diffing 1b2t.mol2.save with 1b2t.mol2 PASSED ============================================================== diffing 1b2t.ac.save with 1b2t.ac PASSED ============================================================== cd antechamber/tp && ./Run.tp diffing tp.mol2.save with tp.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing frcmod.full.save with frcmod.full PASSED ============================================================== cd antechamber/ash && ./Run.ash diffing ash.mol2.save with ash.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== cd antechamber/sustiva && ./Run.sustiva diffing sustiva.mol2.save with sustiva.mol2 PASSED ============================================================== diffing frcmod.save with frcmod PASSED ============================================================== diffing leap.out.save with leap.out PASSED ============================================================== 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 /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12 Running leap tests on ./tleap -> ../../bin/teLeap building force field libraries: '91 ff.. cat: all_amino91.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_amino91.lib with all_amino91.lib possible FAILURE: check all_amino91.lib.dif ============================================================== cat: all_aminoct91.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib possible FAILURE: check all_aminoct91.lib.dif ============================================================== cat: all_aminont91.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_aminont91.lib with all_aminont91.lib possible FAILURE: check all_aminont91.lib.dif ============================================================== cat: all_nucleic91.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib possible FAILURE: check all_nucleic91.lib.dif ============================================================== cat: ions91.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/ions91.lib with ions91.lib possible FAILURE: check ions91.lib.dif ============================================================== '94 ff.. cat: all_amino94.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_amino94.lib with all_amino94.lib possible FAILURE: check all_amino94.lib.dif ============================================================== cat: all_aminoct94.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib possible FAILURE: check all_aminoct94.lib.dif ============================================================== cat: all_aminont94.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_aminont94.lib with all_aminont94.lib possible FAILURE: check all_aminont94.lib.dif ============================================================== diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib possible FAILURE: check all_nucleic94.lib.dif ============================================================== cat: ions94.lib: No such file or directory diffing /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/dat/leap/lib/ions94.lib with ions94.lib possible FAILURE: check ions94.lib.dif ============================================================== 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 possible FAILURE: check all_dna94.top.dif ============================================================== comparing sander energies At line 844 of file ew_box.F90 (unit = 9, file = 'all_dna94.crd') Fortran runtime error: End of file ./Run.tleap: Program error in sander (could be leap input problem) Makefile:55: recipe for target `test.leap' failed make[2]: [test.leap] Error 1 (ignored) cd leap && ./Run.parm7 Creating a new-style (Amber 7) topology file diffing trx.parm7.save with trx.parm7 PASSED ============================================================== diffing trx.solv.parm7.save with trx.solv.parm7 PASSED ============================================================== cd leap && ./Run.cmds Test of several LEaP features diffing sys1.mbondi2.parm7.save with sys1.mbondi2.parm7 PASSED ============================================================== diffing sys2.mbondi2.parm7.save with sys2.mbondi2.parm7 PASSED ============================================================== diffing sys1.mbondi2.rst7.save with sys1.mbondi2.rst7 PASSED ============================================================== diffing sys1_sys2.mbondi.parm7.save with sys1_sys2.mbondi.parm7 PASSED ============================================================== diffing sys1_sys2.mbondi.rst7.save with sys1_sys2.mbondi.rst7 PASSED ============================================================== diffing d_glu.bondi.parm7.save with d_glu.bondi.parm7 PASSED ============================================================== diffing d_glu.bondi.rst7.save with d_glu.bondi.rst7 PASSED ============================================================== cd leap && ./Run.mbondi3 Creating a new-style (Amber 7) topology file with mbondi3 diffing alphabet.mbondi3.parm7.save with alphabet.mbondi3.parm7 PASSED ============================================================== cd leap/glycam && ./Run_tests.bash ** Testing prmtop and inpcrd built by tleap with GLYCAM_06h. ** diffing save.TOP/Aglycons.parm7 with PRMTOP/Aglycons.parm7 PASSED ============================================================== diffing save.TOP/Branches.parm7 with PRMTOP/Branches.parm7 PASSED ============================================================== diffing save.TOP/Chains.parm7 with PRMTOP/Chains.parm7 PASSED ============================================================== diffing save.TOP/SolIon_06h.parm7 with PRMTOP/SolIon_06h.parm7 PASSED ============================================================== diffing save.CRD/Aglycons.rst7 with INPCRD/Aglycons.rst7 possible FAILURE: check INPCRD/Aglycons.rst7.dif ============================================================== diffing save.CRD/Branches.rst7 with INPCRD/Branches.rst7 PASSED ============================================================== diffing save.CRD/Chains.rst7 with INPCRD/Chains.rst7 PASSED ============================================================== diffing save.CRD/SolIon_06h.rst7 with INPCRD/SolIon_06h.rst7 PASSED ============================================================== ** Testing prmtop and inpcrd built by tleap with GLYCAM_06EPb. ** diffing save.TOP/EP.parm7 with PRMTOP/EP.parm7 PASSED ============================================================== diffing save.TOP/Sol_06EPb.parm7 with PRMTOP/Sol_06EPb.parm7 PASSED ============================================================== diffing save.CRD/EP.rst7 with INPCRD/EP.rst7 PASSED ============================================================== diffing save.CRD/Sol_06EPb.rst7 with INPCRD/Sol_06EPb.rst7 PASSED ============================================================== cd resp && ./Run.ade RESP stage 1: diffing ade_1st.out.save with ade_1st.out PASSED ============================================================== diffing ade_1st.pch.save with ade_1st.pch PASSED ============================================================== diffing ade_1st_calc.esp.save with ade_1st_calc.esp PASSED ============================================================== RESP stage 2: diffing ade_1st.chg.save with ade_1st.chg PASSED ============================================================== diffing ade_2nd.out.save with ade_2nd.out PASSED ============================================================== diffing ade_2nd.pch.save with ade_2nd.pch PASSED ============================================================== diffing ade_2nd.chg.save with ade_2nd.chg PASSED ============================================================== cd pbsa_dmp && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== cd pbsa_p3m && ./Run.dmp.min diffing mdout.dmp.min.save with mdout.dmp.min PASSED ============================================================== cd pbsa_bcopt && ./Run.dmp.min bcoption=5 diffing bc5.mdout.dmp.min.save with bc5.mdout.dmp.min PASSED ============================================================== bcoption=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_rot && ./Run.charge.min diffing mdout.charge.min.save with mdout.charge.min 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_ligand && ./Run.t4bnz.min diffing mdout.lig.min.save with mdout.lig.min PASSED ============================================================== cd pbsa_mbfocus && ./test working on ./Run.mb diffing standard.tmp with toverify.tmp PASSED ============================================================== cd pbsa_aug_c2 && ./Run.ion.min diffing save/Li.out.save with Li.out PASSED ============================================================== diffing save/Cl.out.save with Cl.out PASSED ============================================================== diffing save/MG.out.save with MG.out PASSED ============================================================== diffing save/Ca.out.save with Ca.out PASSED ============================================================== cd sas2test && ./Run.ion.min diffing save/Rb.out.2.save with Rb.out.2 PASSED ============================================================== diffing save/IM.out.2.save with IM.out.2 PASSED ============================================================== diffing save/at.out.2.save with at.out.2 PASSED ============================================================== diffing save/Rb.out.5.save with Rb.out.5 possible FAILURE: check Rb.out.5.dif ============================================================== diffing save/IM.out.5.save with IM.out.5 possible FAILURE: check IM.out.5.dif ============================================================== diffing save/at.out.5.save with at.out.5 PASSED ============================================================== cd pbsa_memb_test && ./Run.memb.test initializing variables begining testing for aquaporin_coil parsing option set building input file Running Calculations for aquaporin_coil.mem.out diffing save/aquaporin_coil.mem.out.save with aquaporin_coil.mem.out PASSED ============================================================== parsing option set building input file Running Calculations for aquaporin_coil.wat.out diffing save/aquaporin_coil.wat.out.save with aquaporin_coil.wat.out PASSED ============================================================== parsing option set building input file Running Calculations for aquaporin_coil.vac.out diffing save/aquaporin_coil.vac.out.save with aquaporin_coil.vac.out PASSED ============================================================== cd mmpbsa_py && make test make[3]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/mmpbsa_py' cd EstRAL_Files && ./Run.makeparms diffing com.top with c.top PASSED ============================================================== diffing rec.top with r.top PASSED ============================================================== diffing lig.top with l.top PASSED ============================================================== cd 01_Generalized_Born && ./Run.GB diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing energies.csv.save with energies.csv PASSED ============================================================== cd 02_Poisson_Boltzmann && ./Run.PB diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== diffing energies.csv.save with energies.csv 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.0 PASSED ============================================================== cd 04_Per_Residue_Decomp && ./Run.PerRes diffing DECOMP_ENERGY_VECTORS.csv.save with DECOMP_ENERGY_VECTORS.csv PASSED ============================================================== 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 PASSED ============================================================== cd 08_Stability && ./Run.stability diffing FINAL_RESULTS_MMPBSA1.dat.save with FINAL_RESULTS_MMPBSA1.dat PASSED ============================================================== diffing FINAL_DECOMP_MMPBSA1.csv.save with FINAL_DECOMP_MMPBSA1.csv PASSED ============================================================== diffing FINAL_RESULTS_MMPBSA2.dat.save with FINAL_RESULTS_MMPBSA2.dat PASSED ============================================================== diffing FINAL_DECOMP_MMPBSA2.csv.save with FINAL_DECOMP_MMPBSA2.csv PASSED ============================================================== cd 10_QM_MMGBSA && ./Run.QMMMGBSA diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat PASSED ============================================================== cd 11_3D-RISM && ./Run.rism3d Cannot find /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/bin/rism3d.snglpnt. Cannot run this test. make[3]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/mmpbsa_py' cd parmed/normal_prmtop && ./Run.parmed diffing final.prmtop.save with final.prmtop PASSED ============================================================== diffing prmtop.NBFIX.save with prmtop.NBFIX PASSED ============================================================== diffing prmtop.new_chg.save with prmtop.new_chg PASSED ============================================================== diffing trx.frcmod.save with trx.frcmod PASSED ============================================================== diffing trx.off.save with trx.off PASSED ============================================================== diffing prmtop.mbondi3.save with prmtop.mbondi3 PASSED ============================================================== diffing prmtop.scalenb.save with prmtop.scalenb PASSED ============================================================== diffing prmtop.new_mass.save with prmtop.new_mass PASSED ============================================================== diffing prmtop.new_lj.save with prmtop.new_lj PASSED ============================================================== diffing prmtop.add_AtNum.save with prmtop.add_AtNum PASSED ============================================================== diffing parmed.out.1.save with parmed.out.1 PASSED ============================================================== cd parmed/chamber_prmtop && ./Run.parmed diffing prmtop.new_type.save with prmtop.new_type PASSED ============================================================== diffing prmtop.NBFIX.save with prmtop.NBFIX PASSED ============================================================== diffing prmtop.new_chg.save with prmtop.new_chg PASSED ============================================================== diffing final.prmtop.save with final.prmtop PASSED ============================================================== cd parmed/solvated_prmtop && ./Run.parmed diffing CM_Solute_ions.parm7.save with CM_Solute_ions.parm7 PASSED ============================================================== diffing CM_Solvent_ions.parm7.save with CM_Solvent_ions.parm7 PASSED ============================================================== diffing ions_solvent.parm7.save with ions_solvent.parm7 PASSED ============================================================== diffing CM_stripped.parm7.save with CM_stripped.parm7 PASSED ============================================================== diffing CM_stripped.rst7.save with CM_stripped.rst7 PASSED ============================================================== diffing receptor.prmtop.save with receptor.prmtop PASSED ============================================================== diffing receptor.rst7.save with receptor.rst7 PASSED ============================================================== diffing receptor_excluded.prmtop.save with receptor_excluded.prmtop PASSED ============================================================== cd parmed/change_parms && ./Run.parmed diffing bonded_ions.parm7.save with bonded_ions.parm7 PASSED ============================================================== diffing bonded_ions_changed.parm7.save with bonded_ions_changed.parm7 PASSED ============================================================== 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/ala_ala_ala && ./Runx /bin/rm: No match. diffing chamber.outx.save with chamber.outx PASSED ============================================================== diffing prmtopx.save with prmtopx PASSED ============================================================== diffing inpcrdx.save with inpcrdx 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 ============================================================== cd ./sqm/znh+ && ./Run diffing znh+.pm3.sp.out.save with znh+.pm3.sp.out PASSED ============================================================== diffing znh+.znb.sp.out.save with znh+.znb.sp.out PASSED ============================================================== diffing znh+.pm3.go.out.save with znh+.pm3.go.out PASSED ============================================================== diffing znh+.znb.go.out.save with znh+.znb.go.out PASSED ============================================================== cd ./sqm/h2s && ./Run DFTB SLKO files not found - Skipping DFTB tests... diffing h2s.mndod.sp.out.save with h2s.mndod.sp.out PASSED ============================================================== diffing h2s.pm6.sp.out.save with h2s.pm6.sp.out PASSED ============================================================== diffing h2s.mndod.go.out.save with h2s.mndod.go.out PASSED ============================================================== cd ./sqm/dhplus && ./Run diffing meoh_nh3.pm6-dh+.sp.out.save with meoh_nh3.pm6-dh+.sp.out PASSED ============================================================== diffing meoh_nh3.pm6-dh+.go.out.save with meoh_nh3.pm6-dh+.go.out PASSED ============================================================== cd ./sqm/fecp2 && ./Run diffing fecp2.pm6.sp.out.save with fecp2.pm6.sp.out PASSED ============================================================== cd ./sqm/external_charges && ./Run DFTB SLKO files not found - Skipping DFTB tests... diffing qm_adenine.pm3.sp.out.save with qm_adenine.pm3.sp.out PASSED ============================================================== diffing qm_thymine.pm3.sp.out.save with qm_thymine.pm3.sp.out PASSED ============================================================== if [ -n "" ]; then cd ./rism1d/spc-kh && ./Run.spc; fi if [ -n "" ]; then cd ./rism1d/spc-psen && ./Run.spc-nacl-3; fi if [ -n "" ]; then cd ./rism1d/spc-hnc && ./Run.spc-lj; fi if [ -n "" ]; then cd ./rism1d/spc-mv0 && ./Run.spc; fi if [ -n "" ]; then cd ./rism1d/lj-py && ./Run.lj; fi if [ -n "" ]; then cd ./rism1d/tip3p-kh && ./Run.tip3p; fi cd paramfit && make -k test make[3]: Entering directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/paramfit' cd write_qminput_nma; ./run_test.x *** Create Gaussian Input Files (new prmtop) *** diffing saved_output/prog_out.saved with prog_out.txt possible FAILURE: check prog_out.txt.dif ============================================================== diffing saved_output/Job.0.gjf.saved with Job.0.gjf PASSED ============================================================== diffing saved_output/Job.1.gjf.saved with Job.1.gjf PASSED ============================================================== diffing saved_output/Job.2.gjf.saved with Job.2.gjf PASSED ============================================================== diffing saved_output/Job.3.gjf.saved with Job.3.gjf PASSED ============================================================== diffing saved_output/Job.4.gjf.saved with Job.4.gjf PASSED ============================================================== cd simplex_perfect_fit_NMA; ./run_test.x *** NMA Simplex Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== cd ga_perfect_fit_NMA; ./run_test.x *** NMA Genetic Algorithm Perfect Fit *** diffing saved_output/energy.out.saved with energy.out PASSED ============================================================== make[3]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test/paramfit' Finished test suite for AmberTools at Mon, Apr 02, 2012 11:30:03 PM. make[2]: Leaving directory `/cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/AmberTools/test' 470 file comparisons passed 15 file comparisons failed 1 tests experienced errors Test log file saved as /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/logs/test_at_serial/2012-04-02_22-45-30.log Test diffs file saved as /cygdrive/c/Users/Xiongwu/programs/home/Xiongwu/ambers/amber12/logs/test_at_serial/2012-04-02_22-45-30.diff