make[2]: Entering directory '/home/xxr/amber/amber20/AmberTools/test' Makefile:2: /home/xxr/amber20/amber20///config.h: No such file or directory make[2]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. make[2]: Failed to remake makefile '/home/xxr/amber20/amber20///config.h'. ./test_at_clean.sh cd antechamber && make -k clean make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/antechamber' Cleaning all antechamber test subdirectories: find . -name "*.dif" -print0 | xargs -0 /bin/rm -f /bin/rm -f \ ash/antechamber.out \ ash/sqm.in \ ash/sqm.out \ ash/sqm.pdb \ bondtype/antechamber.out \ c60/antechamber.out \ charmm/antechamber.out \ fluorescein/antechamber.out \ fluorescein/sqm.in \ fluorescein/sqm.out \ fpph/antechamber.out \ guanine_amber/antechamber.out \ guanine_amber/sqm.in \ guanine_amber/sqm.out \ guanine_amber/sqm.pdb \ residuegen/ala_conf1.esp \ residuegen/ala_conf2.esp \ residuegen/ANTECHAMBER_AC.AC \ residuegen/ANTECHAMBER_AC.AC0 \ residuegen/ANTECHAMBER_BOND_TYPE.AC \ residuegen/ANTECHAMBER_BOND_TYPE.AC0 \ residuegen/antechamber.out \ residuegen/ATOMTYPE.INF \ residuegen/esout \ residuegen/espgen.out \ residuegen/NEWPDB.PDB \ residuegen/PREP.INF \ residuegen/punch \ residuegen/QIN \ residuegen/qout \ residuegen/RESIDUE_GEN_MAINCHAIN.DAT \ residuegen/RESIDUE_GEN_RESP.INPUT1 \ residuegen/RESIDUE_GEN_RESP.INPUT2 \ residuegen/RESIDUE_GEN_RESP.OUTPUT1 \ residuegen/RESIDUE_GEN_RESP.OUTPUT2 \ residuegen/RESIDUE_GEN_RESPGEN.DAT \ residuegen/RESIDUE_GEN.AC \ residuegen/residuegen.out \ sustiva/antechamber.out \ sustiva/leap.log \ sustiva/prmtop \ sustiva/sqm.in \ sustiva/sqm.out \ tp/antechamber.out \ tp/sqm.out make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/antechamber' cd mmpbsa_py && make -k clean make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/mmpbsa_py' cd EstRAL_Files && /bin/rm -f ?.top _AnteMMPBSA_* *.dif cd 01_Generalized_Born && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 02_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 03_Alanine_Scanning && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 04_Per_Residue_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 05_Pairwise_Decomp && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 06_NAB_Nmode && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 07_Comprehensive && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 08_Stability && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA*.dat *.dif *.csv cd 09_APBS_Poisson_Boltzmann && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 10_QM_MMGBSA && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 11_3D-RISM && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv cd 12_Membrane_Channel && /bin/rm -f _MMPBSA_* mmpbsa.* FINAL_*_MMPBSA.dat *.dif *.csv make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/mmpbsa_py' cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.clean cd ../src/FEW/examples/test && ./Run.few.clean cd ../src/cpptraj/test && make -k clean make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' Error: In AmberTools and AMBERHOME is not set. Required for tests. Makefile:633: recipe for target 'test.complete' failed make[4]: *** [test.complete] Error 1 Error: In AmberTools and AMBERHOME is not set. Required for tests. Makefile:630: recipe for target 'test.libcpptraj' failed make[4]: *** [test.libcpptraj] Error 1 make[4]: Leaving directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' Makefile:647: recipe for target 'clean' failed make[3]: *** [clean] Error 2 make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' Makefile:353: recipe for target 'clean' failed make[2]: [clean] Error 2 (ignored) cd leap && make -k clean make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/leap' Cleaning all test directories: (find . -name 'leap.log' -o -name 'leap.out' | \ while read dif ;\ do \ rm -f $dif ;\ done ;\ ) /bin/rm -f x.lib lib94.out ions94.log ff94_prm.out ff94_prm.log ff94.log make test.params OPT=clean make[4]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/leap' make[4]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/leap' make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/leap' cd leap/glycam/06j && ./Run.glycam clean cd leap/glycam/06EPb && ./Run.glycam clean cd leap/glycam/06j_10 && ./Run.glycam clean cd leap/glycam/06j_12SB && ./Run.glycam clean Error: AMBERHOME should be defined or else some tests will fail ! Makefile:346: recipe for target 'is_amberhome_defined' failed make[2]: *** [is_amberhome_defined] Error 2 cd nab && make -k test make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/nab' Running test to make dna duplex: ./Run.duplex: 10: ./Run.duplex: /bin/nab: not found ./Run.duplex: Program error Makefile:28: recipe for target 'duplex_test' failed make[3]: *** [duplex_test] Error 1 Running test to computed 3DNA deformation energies: ./Run.deform: 11: ./Run.deform: /bin/nab: not found ./Run.deform: Program error Makefile:31: recipe for target 'deform_test' failed make[3]: *** [deform_test] Error 1 Running Reflexive test: ./Run.reflexive: 11: ./Run.reflexive: /bin/nab: not found ./Run.reflexive: Program error Makefile:34: recipe for target 'reflexive_test' failed make[3]: *** [reflexive_test] Error 1 Running test of sub() and gsub() ./Run.gsub: 10: ./Run.gsub: /bin/nab: not found ./Run.gsub: Program error Makefile:37: recipe for target 'gsub_test' failed make[3]: *** [gsub_test] Error 1 Running test of hashed arrays: ./Run.hashed: 11: ./Run.hashed: /bin/nab: not found ./Run.hashed: Program error Makefile:40: recipe for target 'hashed_test' failed make[3]: *** [hashed_test] Error 1 Running test to compute chemical shifts (this tests many parts of the compiler and libraries) ./Run.shifts: 12: ./Run.shifts: /bin/nab: not found ./Run.shifts: Program error Makefile:43: recipe for target 'shifts_test' failed make[3]: *** [shifts_test] Error 1 Running test to do simple minimization (this tests the molecular mechanics interface) ./Run.sff: 14: ./Run.sff: /bin/nab: not found ./Run.sff: Program error Makefile:46: recipe for target 'sff_test' failed make[3]: *** [sff_test] Error 1 Running test to do simple minimization with shake (this tests the molecular mechanics interface) ./Run.shake: 14: ./Run.shake: /bin/nab: not found ./Run.shake: Program error Makefile:49: recipe for target 'rattle_min_test' failed make[3]: *** [rattle_min_test] Error 1 Running test of fibre-diffraction module ./Run.fd: 13: ./Run.fd: /bin/nab: not found ./Run.fd: Program error Makefile:52: recipe for target 'fd_test' failed make[3]: *** [fd_test] Error 1 Running test to do simple minimization (this tests the generalized Born implementation) ./Run.gb: 14: ./Run.gb: /bin/nab: not found ./Run.gb: Program error Makefile:55: recipe for target 'gb_test' failed make[3]: *** [gb_test] Error 1 Running test to do simple minimization (this tests the generalized Born implementation) ./Run.xfin: 14: ./Run.xfin: /bin/nab: not found ./Run.xfin: Program error Makefile:61: recipe for target 'xfin_test' failed make[3]: *** [xfin_test] Error 1 Running test to do simple minimization (this tests the LCPO surface area) ./Run.gbsa: 14: ./Run.gbsa: /bin/nab: not found ./Run.gbsa: Program error Makefile:64: recipe for target 'gbsa_test' failed make[3]: *** [gbsa_test] Error 1 Running test to do simple minimization (this tests the ao generalized Born implementation) ./Run.gb2: 14: ./Run.gb2: /bin/nab: not found ./Run.gb2: Program error Makefile:67: recipe for target 'gb2_test' failed make[3]: *** [gb2_test] Error 1 Running test to do simple minimization (this tests the ao-2 generalized Born implementation) ./Run.gb5: 14: ./Run.gb5: /bin/nab: not found ./Run.gb5: Program error Makefile:70: recipe for target 'gb5_test' failed make[3]: *** [gb5_test] Error 1 Running test to do simple minimization (this tests the GB Neck implementation; gb==8) ./Run.gb8: 14: ./Run.gb8: /bin/nab: not found ./Run.gb8: Program error Makefile:76: recipe for target 'gb8_test' failed make[3]: *** [gb8_test] Error 1 Running test to do simple minimization (this tests the GB Neck implementation; gb==7) ./Run.gb7: 14: ./Run.gb7: /bin/nab: not found ./Run.gb7: Program error Makefile:73: recipe for target 'gb7_test' failed make[3]: *** [gb7_test] Error 1 Running test to do molecular dynamics with rattle ./Run.rattle_md: 13: ./Run.rattle_md: /bin/nab: not found ./Run.rattle_md: Program error Makefile:79: recipe for target 'rattle_md_test' failed make[3]: *** [rattle_md_test] Error 1 Running test of randomized embedding ./Run.rembed: 11: ./Run.rembed: /bin/nab: not found ./Run.rembed: Program error Makefile:85: recipe for target 'rembed_test' failed make[3]: *** [rembed_test] Error 1 Running test to compute NAB energy of 3dfr minus waters. ./Run.dhfrndpmtx: 13: ./Run.dhfrndpmtx: /bin/nab: not found ./Run.dhfrndpmtx: Program error Makefile:88: recipe for target 'dhfrndpmtx_test' failed make[3]: *** [dhfrndpmtx_test] Error 1 Running test to compute GB Newton-Raphson and normal modes: ./Run.asp: 13: ./Run.asp: /bin/nab: not found ./Run.asp: Program error Makefile:91: recipe for target 'asp_test' failed make[3]: *** [asp_test] Error 1 Running test to compute non-GB Newton-Raphson and normal modes: ./Run.aspnb: 13: ./Run.aspnb: /bin/nab: not found ./Run.aspnb: Program error Makefile:94: recipe for target 'aspnb_test' failed make[3]: *** [aspnb_test] Error 1 Running test to create Amber force-field description ./Run.prm: 14: ./Run.prm: /bin/nab: not found ./Run.prm: Program error Makefile:106: recipe for target 'prm_test' failed make[3]: *** [prm_test] Error 1 Running test to create a simple mmCIF file ./Run.cif: 11: ./Run.cif: /bin/nab: not found ./Run.cif: Program error Makefile:109: recipe for target 'cif_test' failed make[3]: *** [cif_test] Error 1 Running test to do simple xmin minimization ./Run.xmin: 13: ./Run.xmin: /bin/nab: not found ./Run.xmin: Program error Makefile:112: recipe for target 'xmin_test' failed make[3]: *** [xmin_test] Error 1 Running test to do md with netcdf ./Run.gbnetcdf: 13: ./Run.gbnetcdf: /bin/nab: not found ./Run.gbnetcdf: Program error Makefile:58: recipe for target 'gbnetcdf_test' failed make[3]: *** [gbnetcdf_test] Error 1 Running test on netcdf files ./Run.netcdf: 13: ./Run.netcdf: /bin/nab: not found ./Run.netcdf: Program error Makefile:115: recipe for target 'netcdf_test' failed make[3]: *** [netcdf_test] Error 1 Running test for variable 1-4 scaled nonbonded interactions ./Run.variable_14: 13: ./Run.variable_14: /bin/nab: not found ./Run.variable_14: Program error Makefile:100: recipe for target 'variable_14test' failed make[3]: *** [variable_14test] Error 1 Running test to compute GB normal modes using DSYEVD: ./Run.nmode1: 13: ./Run.nmode1: /bin/nab: not found ./Run.nmode1: Program error Makefile:121: recipe for target 'nmode1_test' failed make[3]: *** [nmode1_test] Error 1 Running test to compute GB normal modes using DSAUPD: ./Run.nmode2: 13: ./Run.nmode2: /bin/nab: not found ./Run.nmode2: Program error Makefile:124: recipe for target 'nmode2_test' failed make[3]: *** [nmode2_test] Error 1 Running test to compute Langevin modes: ./Run.nmode3: 13: ./Run.nmode3: /bin/nab: not found ./Run.nmode3: Program error Makefile:127: recipe for target 'nmode3_test' failed make[3]: *** [nmode3_test] Error 1 Running test of the isotropic periodic sum technique ./Run.ips: 13: ./Run.ips: /bin/nab: not found ./Run.ips: Program error Makefile:130: recipe for target 'ips_test' failed make[3]: *** [ips_test] Error 1 Running test to do simple minimization (libpbsa) (this tests the PBSA implementation) ./Run.pbsa: 15: ./Run.pbsa: /bin/nab: not found ./Run.pbsa: Program error Makefile:133: recipe for target 'pbsa_test' failed make[3]: *** [pbsa_test] Error 1 make[3]: Target 'test' not remade because of errors. make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/nab' Makefile:114: recipe for target 'test.nab' failed make[2]: *** [test.nab] Error 2 cd ../src/cpptraj/test && make -k test make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' make test.complete summary make[4]: Entering directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' Error: In AmberTools and AMBERHOME is not set. Required for tests. Makefile:633: recipe for target 'test.complete' failed make[4]: *** [test.complete] Error 1 Error: In AmberTools and AMBERHOME is not set. Required for tests. Makefile:641: recipe for target 'summary' failed make[4]: *** [summary] Error 1 make[4]: Leaving directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' Makefile:618: recipe for target 'test.all' failed make[3]: *** [test.all] Error 2 make[3]: Target 'test' not remade because of errors. make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/src/cpptraj/test' Makefile:136: recipe for target 'test.cpptraj' failed make[2]: *** [test.cpptraj] Error 2 cd pytraj && make make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/pytraj' Makefile:1: /config.h: No such file or directory make[3]: *** No rule to make target '/config.h'. make[3]: Failed to remake makefile '/config.h'. Error: Undefined value for config.h variable SKIP_PYTHON. Makefile:6: recipe for target 'test.pytraj' failed make[3]: *** [test.pytraj] Error 2 make[3]: Target 'fast' not remade because of errors. make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/pytraj' Makefile:142: recipe for target 'test.pytraj' failed make[2]: *** [test.pytraj] Error 2 cd antechamber && make -k test make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/antechamber' cd acdoctor && ./Run.cf antechamber.out: Permission denied. sed: can't read antechamber.out: No such file or directory possible FAILURE: file antechamber.out does not exist. ============================================================== cd bondtype && ./Run.bondtype antechamber.out: Permission denied. ./Run.bondtype: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd fpph && ./Run.fpph antechamber.out: Permission denied. ./Run.fpph: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd fpph && ./Run.fpph_resp antechamber.out: Permission denied. ./Run.fpph_resp: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd g09 && ./Run.g09 antechamber.out: Permission denied. Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd parmchk2 && ./Run.parmchk2 /bin/parmchk2: Command not found. ./Run.parmchk2: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd residuegen && ./Run.ala antechamber.out: Permission denied. ./Run.ala: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd sustiva && ./Run.sustiva antechamber.out: Permission denied. ./Run.sustiva: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd sustiva && ./Run.sustiva_g2 antechamber.out: Permission denied. ./Run.sustiva_g2: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd tp && ./Run.tp antechamber.out: Permission denied. ./Run.tp: Program error Makefile:4: recipe for target 'fast' failed make[3]: [fast] Error 1 (ignored) cd multirespfix && ./Run.multirespfix ./Run.multirespfix: 8: ./Run.multirespfix: cannot create all.esp: Permission denied ./Run.multirespfix: 10: ./Run.multirespfix: cannot create multi_fit.dat: Permission denied ./Run.multirespfix: Program error ./Run.multirespfix: 11: ./Run.multirespfix: cannot create multi_fit.dat: Permission denied ./Run.multirespfix: Program error ./Run.multirespfix: 13: ./Run.multirespfix: cannot create multi_fit.dat: Permission denied ./Run.multirespfix: Program error ./Run.multirespfix: 14: ./Run.multirespfix: cannot create multi_fit.dat: Permission denied ./Run.multirespfix: Program error possible FAILURE: file qout_stage2 does not exist. ============================================================== Checking for errors in logfile ./Run.multirespfix: 19: ./Run.multirespfix: cannot open multi_fit.dat: No such file FAILED Multi conformational fixed charge RESP fit Failed. Check the output files in /home/xxr/amber/amber20/AmberTools/test/antechamber/multirespfix cd c60 && ./Run.c60 antechamber.out: Permission denied. ./Run.c60: Program error Makefile:18: recipe for target 'test' failed make[3]: [test] Error 1 (ignored) cd charge_equlibration && ./Run.equ_charge Step1: run antechamber to generate resp charges with '-eq 0' antechamber.out: Permission denied. ./Run.equ_charge: Program error ./Run.equ_charge: The last command emitted: cat: antechamber.out: No such file or directory Makefile:18: recipe for target 'test' failed make[3]: [test] Error 1 (ignored) cd chemokine && ./Run.1b2t antechamber.out: Permission denied. Makefile:18: recipe for target 'test' failed make[3]: [test] Error 1 (ignored) cd tp && ./Run.tp2 antechamber2.out: Permission denied. ./Run.tp2: Program error Makefile:18: recipe for target 'test' failed make[3]: [test] Error 1 (ignored) cd ash && ./Run.ash antechamber.out: Permission denied. ./Run.ash: Program error Makefile:18: recipe for target 'test' failed make[3]: [test] Error 1 (ignored) cd fluorescein && ./Run.fluorescein antechamber.out: Permission denied. ./Run.fluorescein: Program error Makefile:18: recipe for target 'test' failed make[3]: [test] Error 1 (ignored) cd guanine_amber && ./Run.guanine_amber antechamber.out: Permission denied. ./Run.guanine_amber: Program error Makefile:18: recipe for target 'test' failed make[3]: [test] Error 1 (ignored) make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/antechamber' cd mdgx/1p7e && ./Test.1p7e ./Test.1p7e: line 12: tleap.in: Permission denied ./Test.1p7e: line 21: tleap.out: Permission denied ./Test.1p7e: line 24: mdgx.in: Permission denied ./Test.1p7e: line 57: /bin/mdgx: No such file or directory ./Test.1p7e: line 60: energy.dat: Permission denied ./Test.1p7e: line 61: energy.dat: Permission denied ./Test.1p7e: line 62: energy.dat: Permission denied ./Test.1p7e: line 64: /test/dacdif: No such file or directory cd mdgx/NVTwat && ./Test.nvtwat ./Test.nvtwat: line 11: mdgx.in: Permission denied ./Test.nvtwat: line 45: /bin/mdgx: No such file or directory ./Test.nvtwat: line 48: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 50: temperature.dat: Permission denied ./Test.nvtwat: line 53: /test/dacdif: No such file or directory cd mdgx/MLE && ./Test.mle ./Test.mle: line 11: mdgx.in: Permission denied ./Test.mle: line 53: /bin/mdgx: No such file or directory ./Test.mle: line 56: Eelec.dat: Permission denied ./Test.mle: line 58: Eelec.dat: Permission denied ./Test.mle: line 58: Eelec.dat: Permission denied ./Test.mle: line 58: Eelec.dat: Permission denied ./Test.mle: line 61: /test/dacdif: No such file or directory cd mdgx/Settle && ./Test.settle ./Test.settle: line 11: mdgx.in: Permission denied ./Test.settle: line 46: /bin/mdgx: No such file or directory ./Test.settle: line 49: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 51: etot.dat: Permission denied ./Test.settle: line 54: /test/dacdif: No such file or directory cd mdgx/MCBarostat && ./Test.mcb ./Test.mcb: line 11: mdgx.in: Permission denied ./Test.mcb: line 53: /bin/mdgx: No such file or directory ./Test.mcb: line 56: vol.dat: Permission denied ./Test.mcb: line 58: vol.dat: Permission denied ./Test.mcb: line 58: vol.dat: Permission denied ./Test.mcb: line 61: /test/dacdif: No such file or directory cd mdgx/TIP4P && ./Test.tip4p ./Test.tip4p: line 11: mdgx.in: Permission denied ./Test.tip4p: line 73: /bin/mdgx: No such file or directory ./Test.tip4p: line 76: temperature.dat: Permission denied ./Test.tip4p: line 77: temperature.dat: Permission denied ./Test.tip4p: line 79: /test/dacdif: No such file or directory cd mdgx/ForceCalc && ./Test.frcc ./Test.frcc: line 12: tleap.in: Permission denied ./Test.frcc: line 21: tleap.out: Permission denied ./Test.frcc: line 24: mdgx.in: Permission denied ./Test.frcc: line 60: /bin/mdgx: No such file or directory ./Test.frcc: line 63: frceval.dat: Permission denied grep: forcedump.m: No such file or directory ./Test.frcc: line 64: frceval.dat: Permission denied grep: forcedump.m: No such file or directory ./Test.frcc: line 65: frceval.dat: Permission denied grep: forcedump.m: No such file or directory ./Test.frcc: line 66: frceval.dat: Permission denied grep: forcedump.m: No such file or directory ./Test.frcc: line 67: frceval.dat: Permission denied grep: forcedump.m: No such file or directory ./Test.frcc: line 68: frceval.dat: Permission denied grep: forcedump.m: No such file or directory possible FAILURE: file frceval.dat does not exist. ============================================================== cd mdgx/AddEP && ./Test.addep ./Test.addep: line 11: mdgx.in: Permission denied ./Test.addep: line 66: /bin/mdgx: No such file or directory ./Test.addep: line 69: etot.dat: Permission denied ./Test.addep: line 70: etot.dat: Permission denied ./Test.addep: line 72: /test/dacdif: No such file or directory cd mdgx/QFit && ./Test.qfit ./Test.qfit: line 11: fit.in: Permission denied ./Test.qfit: line 57: /bin/mdgx: No such file or directory ./Test.qfit: line 60: hydrogenQ.dat: Permission denied ./Test.qfit: line 62: /test/dacdif: No such file or directory ./Test.qfit: line 63: /test/dacdif: No such file or directory cd mdgx/Triclinic && ./Test.triclinic ./Test.triclinic: line 11: mdgx.in: Permission denied ./Test.triclinic: line 44: /bin/mdgx: No such file or directory ./Test.triclinic: line 47: temperature.dat: Permission denied ./Test.triclinic: line 49: temperature.dat: Permission denied ./Test.triclinic: line 49: temperature.dat: Permission denied ./Test.triclinic: line 49: temperature.dat: Permission denied ./Test.triclinic: line 49: temperature.dat: Permission denied ./Test.triclinic: line 52: /test/dacdif: No such file or directory cd mdgx/Torsion && ./Test.torsion ./Test.torsion: line 10: Systems.txt: Permission denied ./Test.torsion: line 85: mdgx.in: Permission denied ./Test.torsion: line 94: mdgx.in: Permission denied ./Test.torsion: line 95: mdgx.in: Permission denied ./Test.torsion: line 106: /bin/mdgx: No such file or directory ./Test.torsion: line 107: tmp: Permission denied mv: cannot stat 'tmp': No such file or directory ./Test.torsion: line 111: /AmberTools/test/dacdif: No such file or directory ./Test.torsion: line 112: /AmberTools/test/dacdif: No such file or directory ./Test.torsion: line 115: mdgx.in: Permission denied ./Test.torsion: line 124: mdgx.in: Permission denied ./Test.torsion: line 125: mdgx.in: Permission denied ./Test.torsion: line 140: /bin/mdgx: No such file or directory ./Test.torsion: line 141: trainpa.out: Permission denied ./Test.torsion: line 144: /test/dacdif: No such file or directory ./Test.torsion: line 145: /test/dacdif: No such file or directory cd mdgx/ConfSamp && ./Test.cs ./Test.cs: line 11: mdgx.in: Permission denied ./Test.cs: line 41: /bin/mdgx: No such file or directory ./Test.cs: line 42: extract.txt: Permission denied ./Test.cs: line 43: extract.txt: Permission denied ./Test.cs: line 44: extract.txt: Permission denied ./Test.cs: line 47: /AmberTools/test/dacdif: No such file or directory ./Test.cs: line 48: /AmberTools/test/dacdif: No such file or directory ./Test.cs: line 49: /AmberTools/test/dacdif: No such file or directory ./Test.cs: line 52: tmp: Permission denied mv: cannot stat 'tmp': No such file or directory ./Test.cs: line 54: mdgx.in: Permission denied ./Test.cs: line 68: /bin/mdgx: No such file or directory ./Test.cs: line 69: extractr.txt: Permission denied ./Test.cs: line 70: extractr.txt: Permission denied ./Test.cs: line 71: extractr.txt: Permission denied ./Test.cs: line 74: /AmberTools/test/dacdif: No such file or directory ./Test.cs: line 75: /AmberTools/test/dacdif: No such file or directory cd mdgx/Peptides && ./Test.peptides ./Test.peptides: line 43: mdgx.in: Permission denied ./Test.peptides: line 72: /bin/mdgx: No such file or directory ./Test.peptides: line 17: kine_mts.dat: Permission denied ./Test.peptides: line 21: kine_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: kine_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 17: energy_mts.dat: Permission denied ./Test.peptides: line 23: energy_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: energy_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 17: bond_mts.dat: Permission denied ./Test.peptides: line 19: bond_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: bond_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 17: angl_mts.dat: Permission denied ./Test.peptides: line 21: angl_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: angl_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 17: dihe_mts.dat: Permission denied ./Test.peptides: line 23: dihe_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: dihe_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 17: elec_mts.dat: Permission denied ./Test.peptides: line 19: elec_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: elec_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 17: vdw_mts.dat: Permission denied ./Test.peptides: line 21: vdw_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: vdw_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 17: solv_mts.dat: Permission denied ./Test.peptides: line 23: solv_mts.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: solv_mts.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 89: /test/dacdif: No such file or directory ./Test.peptides: line 94: mdgx.in: Permission denied ./Test.peptides: line 123: /bin/mdgx: No such file or directory ./Test.peptides: line 17: energy_rtt.dat: Permission denied ./Test.peptides: line 23: energy_rtt.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: energy_rtt.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 132: /test/dacdif: No such file or directory ./Test.peptides: line 136: mdgx.in.head: Permission denied ./Test.peptides: line 156: mdgx.in.tail: Permission denied cp: cannot stat 'mdgx.in.head': No such file or directory ./Test.peptides: line 165: mdgx.in: Permission denied ./Test.peptides: line 166: mdgx.in: Permission denied ./Test.peptides: line 167: /bin/mdgx: No such file or directory ./Test.peptides: line 17: solv_igb1.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 23: solv_igb1.dat: Permission denied ./Test.peptides: line 25: solv_igb1.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 172: /test/dacdif: No such file or directory cp: cannot stat 'mdgx.in.head': No such file or directory ./Test.peptides: line 165: mdgx.in: Permission denied ./Test.peptides: line 166: mdgx.in: Permission denied ./Test.peptides: line 167: /bin/mdgx: No such file or directory ./Test.peptides: line 17: solv_igb2.dat: Permission denied ./Test.peptides: line 23: solv_igb2.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: solv_igb2.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 172: /test/dacdif: No such file or directory cp: cannot stat 'mdgx.in.head': No such file or directory ./Test.peptides: line 165: mdgx.in: Permission denied ./Test.peptides: line 166: mdgx.in: Permission denied ./Test.peptides: line 167: /bin/mdgx: No such file or directory ./Test.peptides: line 17: solv_igb5.dat: Permission denied ./Test.peptides: line 23: solv_igb5.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: solv_igb5.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 172: /test/dacdif: No such file or directory cp: cannot stat 'mdgx.in.head': No such file or directory ./Test.peptides: line 165: mdgx.in: Permission denied ./Test.peptides: line 166: mdgx.in: Permission denied ./Test.peptides: line 167: /bin/mdgx: No such file or directory ./Test.peptides: line 17: solv_igb6.dat: Permission denied ./Test.peptides: line 23: solv_igb6.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: solv_igb6.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 172: /test/dacdif: No such file or directory cp: cannot stat 'mdgx.in.head': No such file or directory ./Test.peptides: line 165: mdgx.in: Permission denied ./Test.peptides: line 166: mdgx.in: Permission denied ./Test.peptides: line 167: /bin/mdgx: No such file or directory ./Test.peptides: line 17: solv_igb7.dat: Permission denied ./Test.peptides: line 23: solv_igb7.dat: Permission denied cat: tmp: No such file or directory ./Test.peptides: line 25: solv_igb7.dat: Permission denied rm: cannot remove 'tmp': No such file or directory ./Test.peptides: line 172: /test/dacdif: No such file or directory /bin/rm: cannot remove 'pep*out': No such file or directory /bin/rm: cannot remove 'pep*rst': No such file or directory /bin/rm: cannot remove 'pep*trj': No such file or directory /bin/rm: cannot remove 'trpcage*out': No such file or directory /bin/rm: cannot remove 'trpcage*rst': No such file or directory /bin/rm: cannot remove 'trpcage*trj': No such file or directory /bin/rm: cannot remove 'mdgx.in*': No such file or directory Makefile:169: recipe for target 'test.mdgx' failed make[2]: [test.mdgx] Error 1 (ignored) cd leap && make -k test make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/leap' make test.leap test.params make[4]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/leap' AMBERHOME is set to touch: cannot touch 'x.lib': Permission denied chmod: cannot access 'x.lib': No such file or directory leap.log: Permission denied. Makefile:47: recipe for target 'fast' failed make[4]: [fast] Error 1 (ignored) ./Run.cmds: 14: ./Run.cmds: cannot create leap.in: Permission denied Test of several LEaP features ./Run.cmds: 66: ./Run.cmds: cannot create leap2.log: Permission denied possible FAILURE: file sys1.mbondi2.parm7 does not exist. ============================================================== possible FAILURE: file sys2.mbondi2.parm7 does not exist. ============================================================== possible FAILURE: file sys1.mbondi2.rst7 does not exist. ============================================================== possible FAILURE: file sys1_sys2.mbondi.parm7 does not exist. ============================================================== possible FAILURE: file sys1_sys2.mbondi.rst7 does not exist. ============================================================== possible FAILURE: file d_glu.bondi.parm7 does not exist. ============================================================== possible FAILURE: file d_glu.bondi.rst7 does not exist. ============================================================== possible FAILURE: file alphabet.pdb does not exist. ============================================================== possible FAILURE: file alphabet2.pdb does not exist. ============================================================== possible FAILURE: file alphabet_wet.pdb does not exist. ============================================================== possible FAILURE: file alphabet2_wet.pdb does not exist. ============================================================== ./Run.mbondi3: 10: ./Run.mbondi3: cannot create leap.in: Permission denied Creating a new-style (Amber 7) topology file with mbondi3 ./Run.mbondi3: 31: ./Run.mbondi3: cannot create leap2.log: Permission denied possible FAILURE: file alphabet.mbondi3.parm7 does not exist. ============================================================== ./Run.parm7: 12: ./Run.parm7: cannot create leap.in: Permission denied Creating a new-style (Amber 7) topology file ./Run.parm7: 41: ./Run.parm7: cannot create trx.leapout: Permission denied /bin/mv: cannot stat 'leap.log': No such file or directory possible FAILURE: file trx.leaplog does not exist. ============================================================== possible FAILURE: file trx.leapout does not exist. ============================================================== possible FAILURE: file trx.parm7 does not exist. ============================================================== possible FAILURE: file trx.solv.parm7 does not exist. ============================================================== ./Run.parm7: 49: ./Run.parm7: cannot create gaff_wildcrd.leapout: Permission denied /bin/mv: cannot stat 'leap.log': No such file or directory possible FAILURE: file gaff_wildcrd.leaplog does not exist. ============================================================== possible FAILURE: file gaff_wildcrd.leapout does not exist. ============================================================== possible FAILURE: file gaff_wildcrd.parm7 does not exist. ============================================================== ./Run.addions: 13: ./Run.addions: cannot create leap.in: Permission denied Checking that addIons neutralizes as well as possible ./Run.addions: 100: ./Run.addions: cannot create leap2.log: Permission denied possible FAILURE: file neg_lys_addions.parm7 does not exist. ============================================================== ./Run.addions: 104: ./Run.addions: cannot create check.py: Permission denied Error: The GLYCAM tleap tests require AMBERHOME to be defined. Makefile:52: recipe for target 'test.leap' failed make[4]: [test.leap] Error 1 (ignored) Error: The GLYCAM tleap tests require AMBERHOME to be defined. Makefile:52: recipe for target 'test.leap' failed make[4]: [test.leap] Error 1 (ignored) Error: The GLYCAM tleap tests require AMBERHOME to be defined. Makefile:52: recipe for target 'test.leap' failed make[4]: [test.leap] Error 1 (ignored) Error: The GLYCAM tleap tests require AMBERHOME to be defined. Makefile:52: recipe for target 'test.leap' failed make[4]: [test.leap] Error 1 (ignored) Test application of bond augmentation in advanced force fields. ./Run.1p7e: line 10: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:52: recipe for target 'test.leap' failed make[4]: [test.leap] Error 1 (ignored) AmberTools <= 15 Test OL3 Chi parameters for RNA. ./Run.OL3.sh: line 22: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:21: recipe for target 'test.ol3' failed make[4]: [test.ol3] Error 1 (ignored) AmberTools <= 15 Test Yildirim et al Chi parameters for RNA. ./Run.yildirim.sh: line 22: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:24: recipe for target 'test.yil' failed make[4]: [test.yil] Error 1 (ignored) AmberTools <= 15 Test Yildirim et al Chi parameters for RNA r(GACU). ./Run.GACU.sh: line 20: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:24: recipe for target 'test.yil' failed make[4]: [test.yil] Error 1 (ignored) Test parameters for protein/DNA/RNA system. AmberTools <= 15 ./Run.4PY5.sh: line 21: pp.in: Permission denied ./Run.4PY5.sh: line 72: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:28: recipe for target 'test.ff14sb.ol3.bsc0' failed make[4]: [test.ff14sb.ol3.bsc0] Error 1 (ignored) Test BSC0 parameters. AmberTools <= 15 ./Run.BSC0.sh: line 18: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:31: recipe for target 'test.bsc0' failed make[4]: [test.bsc0] Error 1 (ignored) Test BSC1 parameters. Does not work with AmberTools <= 15 Test OL15 parameters. Does not work with AmberTools <= 15 AmberTools <= 15 Test GB radii assignments. Radii set: bondi ./Run.pbradii.sh: line 22: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:40: recipe for target 'test.pbradii' failed make[4]: [test.pbradii] Error 1 (ignored) Test Bergonzo & Cheatham phosphate b.b. parameters for RNA. ./Run.RNA.LJbb.sh: line 12: leap.in: Permission denied ../TestCommon.sh: line 42: leap.out: Permission denied Program error Makefile:43: recipe for target 'test.rna.ljbb' failed make[4]: [test.rna.ljbb] Error 1 (ignored) make[4]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/leap' make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/leap' cd xtalutil/UnitCell && make make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/xtalutil/UnitCell' ./Run.UnitCell ./Run.UnitCell: 3: ./Run.UnitCell: /bin/UnitCell: not found possible FAILURE: file 2igd_uc.pdb does not exist. ============================================================== make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/xtalutil/UnitCell' cd resp && ./Run.ade RESP stage 1: /bin/resp: Command not found. ./Run.ade: Program error Makefile:163: recipe for target 'test.resp' failed make[2]: *** [test.resp] Error 1 cd reduce && ./Run.reduce ./Run.reduce: 3: ./Run.reduce: cannot create 1ubqH.pdb: Permission denied possible FAILURE: file 1ubqH.pdb does not exist. ============================================================== possible FAILURE: file messages does not exist. ============================================================== cd pbsa_dmp && ./test working on ./Run.dmp.sasopt0 min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp.sasopt0: Program error working on ./Run.dmp.sasopt1 min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp.sasopt1: Program error working on ./Run.dmp.sasopt2 min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp.sasopt2: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_crgview && ./Run.ion.min mdin: Permission denied. /bin/pbsa: Command not found. ./Run.ion.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_bcopt && ./Run.dmp.min min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_saopt && ./Run.dmp.min min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_tri && ./Run.dmp.min min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_rot && ./Run.charge.min min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.charge.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_lpb && ./Run.lsolver.min min.in: Permission denied. bcoption=1 solvopt=1 touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lsolver.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_ipb2 && ./Run.110D.min mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_tsr && ./Run.tsrb.min mdin: Permission denied. /bin/pbsa: Command not found. ./Run.tsrb.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_radi && ./Run.ion.min mdin: Permission denied. /bin/pbsa: Command not found. ./Run.ion.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_npb && ./test pbsa.ncg.bc5 mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error pbsa.nsor.bc5 mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error pbsa.asor.bc5 mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error pbsa.dsor.bc5 mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error pbsa.ntmg.bc5 mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error pbsa.nticcg.bc5 mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error pbsa.nticcg.bc6 mdin: Permission denied. /bin/pbsa: Command not found. ./Run.110D.min: Program error cd pbsa_frc && ./test dbf_0.dgdc min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dgdc.min: Program error dbf_0.polyAT min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyAT.min: Program error dbf_1.dgdc min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dgdc.min: Program error dbf_1.polyAT min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyAT.min: Program error dbf_2.dgdc min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dgdc.min: Program error dbf_2.polyAT min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyAT.min: Program error dbf_3.dgdc min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dgdc.min: Program error dbf_3.polyAT min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyAT.min: Program error cd pbsa_delphi && ./test working on ./Run.1az6.min mdin: Permission denied. /bin/pbsa: Command not found. ./Run.1az6.min: Program error working on ./Run.1az6.pqr mdin: Permission denied. /bin/pbsa: Command not found. ./Run.1az6.pqr: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_ligand && ./Run.t4bnz.min ./Run.t4bnz.min: 15: ./Run.t4bnz.min: cannot create min.in: Permission denied ./Run.t4bnz.min: 34: ./Run.t4bnz.min: /bin/pbsa: not found ./Run.t4bnz.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_ipb4 && ./Run.IIM.min min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.IIM.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_ipb5 && ./Run.ion.min mdin: Permission denied. /bin/pbsa: Command not found. ./Run.ion.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_np3m && ./Run.ion.min mdin: Permission denied. /bin/pbsa: Command not found. ./Run.ion.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_memb_test && ./Run.memb.test mdin: Permission denied. /bin/pbsa: Command not found. ./Run.memb.test: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd pbsa_phiout && ./Run.dmp.min min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp.min: Program error Makefile:188: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd gbnsr6 && ./Run.gbnsr6.min mdin: Permission denied. /bin/gbnsr6: Command not found. ./Run.gbnsr6.min: Program error Makefile:209: recipe for target 'test.gbnsr6' failed make[2]: [test.gbnsr6] Error 1 (ignored) cd parmed/normal_prmtop && ./Run.parmed ./Run.parmed: 13: ./Run.parmed: cannot create parmed.out: Permission denied ./Run.parmed: Program error Makefile:303: recipe for target 'test.parmed' failed make[2]: *** [test.parmed] Error 1 cd elsize && ./Run.elsize elsize_out.trxox: Permission denied. ./Run.elsize: Program error Makefile:220: recipe for target 'test.elsize' failed make[2]: *** [test.elsize] Error 1 cd ./sqm/c2h2 && ./Run /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/ch3f && ./Run /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/nma && ./Run DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/znh+ && ./Run /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/h2s && ./Run DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/dhplus && ./Run /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/fecp2 && ./Run /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/external_charges && ./Run DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... /bin/sqm: Command not found. ./Run: Program error Makefile:240: recipe for target 'test.sqm' failed make[2]: [test.sqm] Error 1 (ignored) cd ./sqm/dftb3 && ./Run DFTB3 3ob-3-1 SLKO files not found - Skipping DFTB tests... 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/tip3p-kh && ./Run.tip3p; fi cd rism3d.periodic/4lzta && ./Run.4lzta.kh.pme ./Run.4lzta.kh.pme: 22: ./Run.4lzta.kh.pme: cannot create 4lzta_5.pse1.pme.r3d: Permission denied ./Run.4lzta.kh.pme: 32: ./Run.4lzta.kh.pme: cannot create erism.pme.out: Permission denied grep: 4lzta_5.pse1.pme.r3d: No such file or directory possible FAILURE: file erism.pme.out does not exist. ============================================================== cd rism3d.periodic/1ahoa && ./Run.1ahoa.kh.pme ./Run.1ahoa.kh.pme: 23: ./Run.1ahoa.kh.pme: cannot create 1ahoa.kh.pme.r3d: Permission denied ./Run.1ahoa.kh.pme: 30: ./Run.1ahoa.kh.pme: cannot create erism.pme.out: Permission denied grep: 1ahoa.kh.pme.r3d: No such file or directory possible FAILURE: file erism.pme.out does not exist. ============================================================== cd paramfit && make -k test make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/paramfit' cd write_qminput_nma; ./run_test.x *** Create Gaussian Input Files (new prmtop) *** prog_out.txt: Permission denied. ./run_test.x: Program error Makefile:2: recipe for target 'test' failed make[3]: *** [test] Error 1 make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/paramfit' Makefile:160: recipe for target 'test.paramfit' failed make[2]: *** [test.paramfit] Error 2 cd ../src/mm_pbsa/Examples && AMBER_SOURCE= ./Run.mmpbsa.test /AmberTools/src/mm_pbsa/Examples: No such file or directory. Makefile:294: recipe for target 'test.mm_pbsa' failed make[2]: *** [test.mm_pbsa] Error 1 cd ../src/FEW/examples/test && AMBER_SOURCE= ./Run.few.test ######################################################################### PERFORMING FEW TESTS If all of the tests below fail then check the system specific path to the locally installed Perl libraries. For details on test issues and on how to fix them read: /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/few.log CLEANING mkdir: cannot create directory ‘/home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files’: Permission denied mkdir: cannot create directory ‘/home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/structs’: Permission denied /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/step1_setup_resp_3trj_MDs: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/step2_setup_resp_3trj_MDs: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/mmpbsa_resp_1trj: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/lie_resp: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/TI_setup_step1.in: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/TI_setup_step2A.in: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/TI_setup_step2B.in: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/TI_setup_step3.in: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/setup_am1_1trj_membraneMDs: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/mmpbsa_am1_1trj_ImplicitMembrane: No such file or directory. /home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/c_files/mmpbsa_prot_1trj_pb3_gb0_snapshots1-2_ImplicitMembrane: No such file or directory. cp: cannot create regular file '/home/xxr/amber/amber20/AmberTools/src/FEW/examples/test/structs': Permission denied PERFORMING TEST 01: Step1 of RESP charge calculation few.log: Permission denied. ./Run.few.test: Program error Makefile:297: recipe for target 'test.FEW' failed make[2]: *** [test.FEW] Error 1 cd cphstats && ./Run.cphstats ./Run.cphstats: 20: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 21: ./Run.cphstats: /bin/cphstats: not found possible FAILURE: file md2_cpout.pH_2.00 does not exist. ============================================================== possible FAILURE: file md3_cpout.pH_4.50 does not exist. ============================================================== ./Run.cphstats: 29: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 30: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 31: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 32: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 33: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 34: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 35: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 36: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 37: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 38: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 39: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 40: ./Run.cphstats: /bin/cphstats: not found possible FAILURE: file pH_2.00.calcpka does not exist. ============================================================== possible FAILURE: file pH_2.50.calcpka does not exist. ============================================================== possible FAILURE: file pH_3.00.calcpka does not exist. ============================================================== possible FAILURE: file pH_3.50.calcpka does not exist. ============================================================== possible FAILURE: file pH_4.00.calcpka does not exist. ============================================================== possible FAILURE: file pH_4.50.calcpka does not exist. ============================================================== possible FAILURE: file pH_5.00.calcpka does not exist. ============================================================== possible FAILURE: file pH_5.50.calcpka does not exist. ============================================================== possible FAILURE: file pH_6.00.calcpka does not exist. ============================================================== possible FAILURE: file pH_6.50.calcpka does not exist. ============================================================== possible FAILURE: file pH_7.00.calcpka does not exist. ============================================================== possible FAILURE: file pH_7.50.calcpka does not exist. ============================================================== gzip: md?_cpout.pH_2.00: No such file or directory ./Run.cphstats: 59: ./Run.cphstats: cannot create cphstats_output.txt: Permission denied possible FAILURE: file pH_2.00.calcpka does not exist. ============================================================== possible FAILURE: file cphstats_output.txt does not exist. ============================================================== ./Run.cphstats: 66: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 68: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 70: ./Run.cphstats: /bin/cphstats: not found possible FAILURE: file running_avgs.dat does not exist. ============================================================== possible FAILURE: file running_avg.dat does not exist. ============================================================== possible FAILURE: file running_pKa.dat does not exist. ============================================================== ./Run.cphstats: 78: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 80: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 82: ./Run.cphstats: /bin/cphstats: not found possible FAILURE: file chunk.dat does not exist. ============================================================== possible FAILURE: file chunk_deprot.dat does not exist. ============================================================== possible FAILURE: file chunk_pka.dat does not exist. ============================================================== ./Run.cphstats: 90: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 92: ./Run.cphstats: /bin/cphstats: not found ./Run.cphstats: 95: ./Run.cphstats: /bin/cphstats: not found possible FAILURE: file cumulative.dat does not exist. ============================================================== possible FAILURE: file cumulative_deprot.dat does not exist. ============================================================== possible FAILURE: file cumulative_pka.dat does not exist. ============================================================== ./Run.cphstats: 104: ./Run.cphstats: /bin/cphstats: not found possible FAILURE: file pop.dat does not exist. ============================================================== ./Run.cphstats: 110: ./Run.cphstats: /bin/cphstats: not found possible FAILURE: file conditional.dat does not exist. ============================================================== possible FAILURE: file conditional_chunks.dat does not exist. ============================================================== ./Run.cphstats: 119: ./Run.cphstats: cannot create cphstats_output.cpe.txt: Permission denied possible FAILURE: file cphstats_output.cpe.txt does not exist. ============================================================== cd cestats && ./Run.cestats Could not find cestats in the previous directory. Re-install, then test again. Makefile:237: recipe for target 'test.cestats' failed make[2]: [test.cestats] Error 1 (ignored) cd charmmlipid2amber && ./Run.charmmlipid2amber ./Run.charmmlipid2amber: 28: ./Run.charmmlipid2amber: /bin/charmmlipid2amber.py: not found ./Run.charmmlipid2amber: Program error Makefile:331: recipe for target 'test.charmmlipid2amber' failed make[2]: *** [test.charmmlipid2amber] Error 1 cd cpinutil && ./Run.cpin cpin1: Permission denied. ./Run.cpin: Program error Makefile:313: recipe for target 'test.cpinutil' failed make[2]: *** [test.cpinutil] Error 1 cd ceinutil && ./Run.cein cein1: Permission denied. ./Run.cein: Program error Makefile:316: recipe for target 'test.ceinutil' failed make[2]: *** [test.ceinutil] Error 1 cd cpeinutil && ./Run.cpein cpein1: Permission denied. ./Run.cpein: Program error Makefile:319: recipe for target 'test.cpeinutil' failed make[2]: *** [test.cpeinutil] Error 1 cd genremdinputs && ./Run.genremdinputs output1.1d.dat: Permission denied. ./Run.genremdinputs: Program error Makefile:322: recipe for target 'test.genremdinputs' failed make[2]: *** [test.genremdinputs] Error 1 cd fitpkaeo && ./Run.fitpkaeo output.pka.dat: Permission denied. ./Run.fitpkaeo: Program error Makefile:325: recipe for target 'test.fitpkaeo' failed make[2]: *** [test.fitpkaeo] Error 1 cd fixremdcouts && ./Run.fixremdcouts /bin/fixremdcouts.py: Command not found. ./Run.fixremdcouts: Program error Makefile:328: recipe for target 'test.fixremdcouts' failed make[2]: *** [test.fixremdcouts] Error 1 cd pymsmt/mcpb/g03-ff14SB && ./Run.pymsmt ./Run.pymsmt: 12: ./Run.pymsmt: cannot create mcpbpy.out: Permission denied ./Run.pymsmt: Program error Makefile:145: recipe for target 'test.pymsmt' failed make[2]: *** [test.pymsmt] Error 1 cd packmol_memgen/ && ./Run.packmol-memgen running memembed ./Run.packmol-memgen: 16: ./Run.packmol-memgen: cannot create memembed.log: Permission denied ./Run.packmol-memgen: Program error grep: memembed.log: No such file or directory Possible FAILURE MEMEMBED Failed. Check the output files in /home/xxr/amber/amber20/AmberTools/test/packmol_memgen running simple packmol-memgen run ./Run.packmol-memgen: 36: ./Run.packmol-memgen: cannot create packmol-memgen.out: Permission denied ./Run.packmol-memgen: Program error grep: packmol-memgen.out: No such file or directory Possible FAILURE PACKMOL-MEMGEN Failed. Check the output files in /home/xxr/amber/amber20/AmberTools/test/packmol_memgen cd mmpbsa_py && make test make[3]: Entering directory '/home/xxr/amber/amber20/AmberTools/test/mmpbsa_py' ./Run.exist /bin/MMPBSA.py does not exist! ./Run.exist: Program error Makefile:4: recipe for target 'fast' failed make[3]: *** [fast] Error 1 cd EstRAL_Files && ./Run.makeparms Error: AMBERHOME must be set! Makefile:45: recipe for target 'ANTE-MMPBSA' failed make[3]: [ANTE-MMPBSA] Error 1 (ignored) cd 01_Generalized_Born && ./Run.GB Error: AMBERHOME must be set! Makefile:11: recipe for target 'GB' failed make[3]: [GB] Error 1 (ignored) cd 02_Poisson_Boltzmann && ./Run.PB Error: AMBERHOME must be set! Makefile:14: recipe for target 'PB' failed make[3]: [PB] Error 1 (ignored) cd 03_Alanine_Scanning && ./Run.ALA Error: AMBERHOME must be set! Makefile:17: recipe for target 'ALA' failed make[3]: [ALA] Error 1 (ignored) cd 10_QM_MMGBSA && ./Run.QMMMGBSA This test requires sander and can only be run with Amber12 installed. cd 11_3D-RISM && ./Run.rism3d Error: AMBERHOME must be set! Makefile:39: recipe for target '3DRISM' failed make[3]: [3DRISM] Error 1 (ignored) cd 12_Membrane_Channel && ./Run.mem Error: AMBERHOME must be set! Makefile:42: recipe for target 'MEM' failed make[3]: [MEM] Error 1 (ignored) make[3]: Target 'test' not remade because of errors. make[3]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test/mmpbsa_py' Makefile:291: recipe for target 'test.mmpbsa' failed make[2]: *** [test.mmpbsa] Error 2 make[2]: Target 'test.serial' not remade because of errors. make[2]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test' make[2]: Entering directory '/home/xxr/amber/amber20/test' Makefile:4: /home/xxr/amber20/amber20///config.h: No such file or directory make[2]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. make[2]: Failed to remake makefile '/home/xxr/amber20/amber20///config.h'. cd dmp && ./Run.dmp min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dmp: Program error Makefile:131: recipe for target 'test.sander.BASIC.nopar' failed make[2]: [test.sander.BASIC.nopar] Error 1 (ignored) cd adenine && ./Run.adenine min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.adenine: Program error Makefile:131: recipe for target 'test.sander.BASIC.nopar' failed make[2]: [test.sander.BASIC.nopar] Error 1 (ignored) cd variable_14 && ./Run.variable_14_igb1 mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.variable_14_igb1: Program error Makefile:131: recipe for target 'test.sander.BASIC.nopar' failed make[2]: [test.sander.BASIC.nopar] Error 1 (ignored) cd rdc && ./Run.nef /home/xxr/amber20/amber20///bin/nef_to_RST: Command not found. ./Run.nef: Program error Makefile:131: recipe for target 'test.sander.BASIC.nopar' failed make[2]: [test.sander.BASIC.nopar] Error 1 (ignored) cd cytosine && ./Run.cytosine in.md: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.cytosine: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nonper && ./Run.nonper gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.nonper: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nonper && ./Run.egb6 gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.egb6: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nonper && ./Run.nonper.belly gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.nonper.belly: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nonper && ./Run.nonper.belly.mask gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nonper && ./Run.nonper.min gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.nonper.min: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nonper && ./Run.cap /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.cap: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nonper && ./Run.nonper.nocut gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.nonper.nocut: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tip4p && ./Run.tip4p mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip4p: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tip4p && ./Run.tip4p_mcbar mdin: Permission denied. mdin2: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip4p_mcbar: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tip4p && ./Run.tip4p_nve mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip4p_nve: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tip5p && ./Run.tip5p mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip5p: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tip5p && ./Run.tip5p_nve mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip5p_nve: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd 4096wat && ./Run.pure_wat gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pure_wat: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd 4096wat && ./Run.pure_wat_fswitch gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pure_wat_fswitch: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd 4096wat && ./Run.pure_wat_nmr_temp_reg gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pure_wat_nmr_temp_reg: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd 4096wat && ./Run.vrand gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.vrand: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd 4096wat && ./Run.frcdmp ./Run.frcdmp: 14: ./Run.frcdmp: cannot create gbin: Permission denied ./Run.frcdmp: 28: ./Run.frcdmp: /home/xxr/amber20/amber20///bin/sander: not found ./Run.frcdmp: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd 4096wat_oct && ./Run.pure_wat_oct mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pure_wat_oct: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd dhfr && ./Run.dhfr && ./Run.dhfr prmtop_an gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.dhfr: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd dhfr && ./Run.dhfr.noboxinfo gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. possible FAILURE: file mdout.dhfr.noboxinfo does not exist. ============================================================== cd dhfr && ./Run.dhfr.noshake gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr.noshake: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd dhfr && ./Run.dhfr.bussi gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.dhfr.bussi: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd dhfr && ./Run.dhfr.min gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr.min: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd dhfr && ./Run.dhfr.min_prcg gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr.min_prcg: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd dhfr && ./Run.dhfr.xmin gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr.xmin: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd ff14ipq && ./Run.ff14ipq mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.ff14ipq: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd variable_14 && ./Run.variable_14_ntb1 mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.variable_14_ntb1: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd polarizable_water && ./Run.pol_wat /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pol_wat: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd ubiquitin && ./Run.ubiquitin mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.ubiquitin: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd dna_pol && ./Run.dna_pol mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.dna_pol: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd trx && ./Run.trx gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.trx: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd trx && ./Run.trx.cpln gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.trx.cpln: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd rdc && ./Run.dip mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.dip: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd rdc && ./Run.csa mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.csa: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd rdc && ./Run.csa_min mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.csa_min: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd rdc && ./Run.nmr mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.nmr: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd pcsa && ./Run.dip mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.dip: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd pcsa && ./Run.csa mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.csa: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd pcsa && ./Run.csa2 mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.csa2: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd pcsa && ./Run.csa_min mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.csa_min: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tgtmd/change_target && ./Run.tgtmd touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tgtmd: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tgtmd/change_target.rms && ./Run.tgtmd touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tgtmd: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tgtmd/change_target.ntr && ./Run.tgtmd touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tgtmd: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tgtmd/conserve_ene && ./Run.tgtmd touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tgtmd: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tgtmd/minimize && ./Run.tgtmin touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tgtmin: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd tgtmd/PME && ./Run.tgtPME touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tgtPME: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd mtmdtest && ./Run.mtmdtest SANDER: Multiply-targeted MD, new to AMBER 11 Tested on an RNA duplex. mtmdin: Permission denied. sample_mtmd_file.mtmd: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.mtmdtest: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd trajene && ./Run.trajene touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.trajene: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd trajene_box && ./Run.trajene touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.trajene: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd trajene_netcdf && ./Run.trajene Build does not include NetCDF support - skipping this test. cd alp && ./Run.alp gbin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.alp: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd umbrella && ./Run.umbrella gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.umbrella: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd noesy && ./Run.noesy mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.noesy: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd jar && ./Run.jarz gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.jarz: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd plane_plane_restraint && ./Run.dinuc_plpt SANDER: Dinucleoside restrained with new plane-point angle restraint that was defined with new natural language restraint input. gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.dinuc_plpt: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd plane_plane_restraint && ./Run.dinuc_pln SANDER: Dinucleoside restrained with new plane-plane angle restraint that was defined with new natural language restraint input. gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.dinuc_pln: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd iwrap2 && ./Run.iwrap2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.iwrap2: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd idecomp1 && ./run_idecomp1.sh decomp.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./run_idecomp1.sh: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd idecomp4 && ./run_idecomp4.sh decomp.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./run_idecomp4.sh: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd bintraj && ./Run.bintraj mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.bintraj: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd netcdf && make -k test OPT= make[3]: Entering directory '/home/xxr/amber/amber20/test/netcdf' ./runmd.sh: line 15: md.in: Permission denied Netcdf MD Restart Write Test ./runmd.sh: line 32: /home/xxr/amber20/amber20///bin/sander: No such file or directory ./runmd.sh: Program error Makefile:6: recipe for target 'mdrstwrite' failed make[3]: [mdrstwrite] Error 1 (ignored) ./runmin.sh: line 15: min.in: Permission denied Netcdf Minimization Restart Write Test ./runmin.sh: line 28: /home/xxr/amber20/amber20///bin/sander: No such file or directory ./runmin.sh: Program error Makefile:9: recipe for target 'minrstwrite' failed make[3]: [minrstwrite] Error 1 (ignored) ./runmd.sh: line 16: md.in: Permission denied Restrained MD with netcdf Restart Reference Coords Test ./runmd.sh: line 34: /home/xxr/amber20/amber20///bin/sander: No such file or directory ./runmd.sh: Program error Makefile:12: recipe for target 'ncrefmd' failed make[3]: [ncrefmd] Error 1 (ignored) Netcdf MD restart read test, ntx=5 ./runmd.sh: line 20: md.in: Permission denied ./runmd.sh: line 35: /home/xxr/amber20/amber20///bin/sander: No such file or directory ./runmd.sh: Program error Makefile:15: recipe for target 'ntx5' failed make[3]: [ntx5] Error 1 (ignored) Netcdf MD restart read test, ntx=1 ./runmd.sh: line 20: md.in: Permission denied ./runmd.sh: line 35: /home/xxr/amber20/amber20///bin/sander: No such file or directory ./runmd.sh: Program error Makefile:18: recipe for target 'ntx1' failed make[3]: [ntx1] Error 1 (ignored) make[3]: Leaving directory '/home/xxr/amber/amber20/test/netcdf' cd velocity_write && ./Run.vel1 ./Run.vel1: 23: ./Run.vel1: cannot create vel1.in: Permission denied ./Run.vel1: 39: ./Run.vel1: /home/xxr/amber20/amber20///bin/sander: not found ./Run.vel1: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd velocity_write && ./Run.vel2 ./Run.vel2: 1: ./Run.vel2: /home/xxr/amber20/amber20///bin/sander: not found ./Run.vel2: 30: ./Run.vel2: cannot create vel2.in: Permission denied ./Run.vel2: 46: ./Run.vel2: /home/xxr/amber20/amber20///bin/sander: not found ./Run.vel2: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd csurften && ./Run.csurften_z-dir mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.csurften_z-dir: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd csurften && ./Run.csurften_z-dir_npt_3 mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.csurften_z-dir_npt_3: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd linear_interaction_energy && ./Run.lie min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lie: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd nmropt && make all make[3]: Entering directory '/home/xxr/amber/amber20/test/nmropt' cd gb/angle && ./Run.nmropt_1angle_gb ./Run.nmropt_1angle_gb: 17: ./Run.nmropt_1angle_gb: cannot create mdin: Permission denied ./Run.nmropt_1angle_gb: 37: ./Run.nmropt_1angle_gb: cannot create angle_gb.RST: Permission denied ./Run.nmropt_1angle_gb: 43: ./Run.nmropt_1angle_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1angle_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/distance && ./Run.dist_gb ./Run.dist_gb: 17: ./Run.dist_gb: cannot create mdin: Permission denied ./Run.dist_gb: 43: ./Run.dist_gb: cannot create dist_gb.RST: Permission denied ./Run.dist_gb: 49: ./Run.dist_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.dist_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/distance_COM && ./Run.distCOM_gb ./Run.distCOM_gb: 17: ./Run.distCOM_gb: cannot create mdin: Permission denied ./Run.distCOM_gb: 43: ./Run.distCOM_gb: cannot create distCOM_gb.RST: Permission denied ./Run.distCOM_gb: 49: ./Run.distCOM_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.distCOM_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/jar_distance && ./Run.jar_gb ./Run.jar_gb: 17: ./Run.jar_gb: cannot create mdin: Permission denied ./Run.jar_gb: 43: ./Run.jar_gb: cannot create dist_gb.RST: Permission denied ./Run.jar_gb: 47: ./Run.jar_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/jar_distance_COM && ./Run.jar_gb ./Run.jar_gb: 17: ./Run.jar_gb: cannot create mdin: Permission denied ./Run.jar_gb: 43: ./Run.jar_gb: cannot create distCOM_gb.RST: Permission denied ./Run.jar_gb: 48: ./Run.jar_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/jar_torsion && ./Run.jar_torsion ./Run.jar_torsion: 17: ./Run.jar_torsion: cannot create mdin: Permission denied ./Run.jar_torsion: 36: ./Run.jar_torsion: cannot create jartorsion_gb.RST: Permission denied ./Run.jar_torsion: 45: ./Run.jar_torsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_torsion: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/nmropt_1_torsion && ./Run.nmropt_1_torsion ./Run.nmropt_1_torsion: 17: ./Run.nmropt_1_torsion: cannot create mdin: Permission denied ./Run.nmropt_1_torsion: 36: ./Run.nmropt_1_torsion: cannot create torsion_gb.RST: Permission denied ./Run.nmropt_1_torsion: 46: ./Run.nmropt_1_torsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1_torsion: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/tautp && ./Run.nmropt_1tautp_gb ./Run.nmropt_1tautp_gb: 17: ./Run.nmropt_1tautp_gb: cannot create mdin: Permission denied ./Run.nmropt_1tautp_gb: 37: ./Run.nmropt_1tautp_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1tautp_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/temp && ./Run.nmropt_1temp_gb ./Run.nmropt_1temp_gb: 17: ./Run.nmropt_1temp_gb: cannot create mdin: Permission denied ./Run.nmropt_1temp_gb: 37: ./Run.nmropt_1temp_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1temp_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd gb/angle_torsion_com/ && ./Run.angdihCOM_gb ./Run.angdihCOM_gb: 17: ./Run.angdihCOM_gb: cannot create mdin: Permission denied ./Run.angdihCOM_gb: 43: ./Run.angdihCOM_gb: cannot create angtorCOM_gb.RST: Permission denied ./Run.angdihCOM_gb: 64: ./Run.angdihCOM_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.angdihCOM_gb: Program error Makefile:13: recipe for target 'pmemd_compat_gb' failed make[3]: [pmemd_compat_gb] Error 1 (ignored) cd pme/angle && ./Run.nmropt_1angle_pbc ./Run.nmropt_1angle_pbc: 17: ./Run.nmropt_1angle_pbc: cannot create mdin: Permission denied ./Run.nmropt_1angle_pbc: 38: ./Run.nmropt_1angle_pbc: cannot create angle_pbc.RST: Permission denied ./Run.nmropt_1angle_pbc: 44: ./Run.nmropt_1angle_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1angle_pbc: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/distance && ./Run.dist_pbc ./Run.dist_pbc: 17: ./Run.dist_pbc: cannot create mdin: Permission denied ./Run.dist_pbc: 47: ./Run.dist_pbc: cannot create dist_pbc.RST: Permission denied ./Run.dist_pbc: 52: ./Run.dist_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.dist_pbc: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/distance_COM && ./Run.distCOM_pbc ./Run.distCOM_pbc: 17: ./Run.distCOM_pbc: cannot create mdin: Permission denied ./Run.distCOM_pbc: 47: ./Run.distCOM_pbc: cannot create distCOM_pbc.RST: Permission denied ./Run.distCOM_pbc: 53: ./Run.distCOM_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.distCOM_pbc: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/jar_torsion && ./Run.jar_torsion ./Run.jar_torsion: 17: ./Run.jar_torsion: cannot create mdin: Permission denied ./Run.jar_torsion: 39: ./Run.jar_torsion: cannot create jartorsion_pbc.RST: Permission denied ./Run.jar_torsion: 48: ./Run.jar_torsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_torsion: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/jar_distance && ./Run.jar_pbc ./Run.jar_pbc: 17: ./Run.jar_pbc: cannot create mdin: Permission denied ./Run.jar_pbc: 47: ./Run.jar_pbc: cannot create dist_pbc.RST: Permission denied ./Run.jar_pbc: 52: ./Run.jar_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_pbc: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/jar_distance_COM && ./Run.jar_pbc ./Run.jar_pbc: 17: ./Run.jar_pbc: cannot create mdin: Permission denied ./Run.jar_pbc: 47: ./Run.jar_pbc: cannot create distCOM_pbc.RST: Permission denied ./Run.jar_pbc: 52: ./Run.jar_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_pbc: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/nmropt_1_torsion && ./Run.nmropt_1_torsion ./Run.nmropt_1_torsion: 17: ./Run.nmropt_1_torsion: cannot create mdin: Permission denied ./Run.nmropt_1_torsion: 39: ./Run.nmropt_1_torsion: cannot create torsion_pbc.RST: Permission denied ./Run.nmropt_1_torsion: 49: ./Run.nmropt_1_torsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1_torsion: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/tautp && ./Run.nmropt_1tautp_pbc ./Run.nmropt_1tautp_pbc: 17: ./Run.nmropt_1tautp_pbc: cannot create mdin: Permission denied ./Run.nmropt_1tautp_pbc: 39: ./Run.nmropt_1tautp_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1tautp_pbc: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/temp && ./Run.nmropt_1temp_pbc ./Run.nmropt_1temp_pbc: 17: ./Run.nmropt_1temp_pbc: cannot create mdin: Permission denied ./Run.nmropt_1temp_pbc: 39: ./Run.nmropt_1temp_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1temp_pbc: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd pme/angle_torsion_com/ && ./Run.angdihCOM ./Run.angdihCOM: 17: ./Run.angdihCOM: cannot create mdin: Permission denied ./Run.angdihCOM: 47: ./Run.angdihCOM: cannot create angtorCOM.RST: Permission denied ./Run.angdihCOM: 68: ./Run.angdihCOM: /home/xxr/amber20/amber20///bin/sander: not found ./Run.angdihCOM: Program error Makefile:34: recipe for target 'pmemd_compat_pme' failed make[3]: [pmemd_compat_pme] Error 1 (ignored) cd gb/2xangle && ./Run.nmropt_1_2xangle_gb ./Run.nmropt_1_2xangle_gb: 17: ./Run.nmropt_1_2xangle_gb: cannot create mdin: Permission denied ./Run.nmropt_1_2xangle_gb: 37: ./Run.nmropt_1_2xangle_gb: cannot create 2xangle_gb.RST: Permission denied ./Run.nmropt_1_2xangle_gb: 45: ./Run.nmropt_1_2xangle_gb: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1_2xangle_gb: Program error Makefile:25: recipe for target 'pmemd_incompat_gb' failed make[3]: [pmemd_incompat_gb] Error 1 (ignored) cd gb/jar_comtorsion && ./Run.jar_comtorsion ./Run.jar_comtorsion: 17: ./Run.jar_comtorsion: cannot create mdin: Permission denied ./Run.jar_comtorsion: 37: ./Run.jar_comtorsion: cannot create jartorsion_com_gb.RST: Permission denied ./Run.jar_comtorsion: 47: ./Run.jar_comtorsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_comtorsion: Program error Makefile:25: recipe for target 'pmemd_incompat_gb' failed make[3]: [pmemd_incompat_gb] Error 1 (ignored) cd gb/jar_lcod && ./Run.lcod_jar ./Run.lcod_jar: 17: ./Run.lcod_jar: cannot create mdin: Permission denied ./Run.lcod_jar: 39: ./Run.lcod_jar: cannot create lcod.RST: Permission denied ./Run.lcod_jar: 46: ./Run.lcod_jar: /home/xxr/amber20/amber20///bin/sander: not found ./Run.lcod_jar: Program error Makefile:25: recipe for target 'pmemd_incompat_gb' failed make[3]: [pmemd_incompat_gb] Error 1 (ignored) cd gb/jar_lcod_dist && ./Run.jar_lcod ./Run.jar_lcod: 17: ./Run.jar_lcod: cannot create mdin: Permission denied ./Run.jar_lcod: 39: ./Run.jar_lcod: cannot create lcod.RST: Permission denied ./Run.jar_lcod: 49: ./Run.jar_lcod: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_lcod: Program error Makefile:25: recipe for target 'pmemd_incompat_gb' failed make[3]: [pmemd_incompat_gb] Error 1 (ignored) cd gb/lcod && ./Run.lcod ./Run.lcod: 17: ./Run.lcod: cannot create mdin: Permission denied ./Run.lcod: 38: ./Run.lcod: cannot create lcod.RST: Permission denied ./Run.lcod: 44: ./Run.lcod: /home/xxr/amber20/amber20///bin/sander: not found ./Run.lcod: Program error Makefile:25: recipe for target 'pmemd_incompat_gb' failed make[3]: [pmemd_incompat_gb] Error 1 (ignored) cd gb/lcod_com && ./Run.lcod_com ./Run.lcod_com: 17: ./Run.lcod_com: cannot create mdin: Permission denied ./Run.lcod_com: 38: ./Run.lcod_com: cannot create lcod.RST: Permission denied ./Run.lcod_com: 48: ./Run.lcod_com: /home/xxr/amber20/amber20///bin/sander: not found ./Run.lcod_com: Program error Makefile:25: recipe for target 'pmemd_incompat_gb' failed make[3]: [pmemd_incompat_gb] Error 1 (ignored) cd gb/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion ./Run.nmropt_1_2xtorsion: 17: ./Run.nmropt_1_2xtorsion: cannot create mdin: Permission denied ./Run.nmropt_1_2xtorsion: 36: ./Run.nmropt_1_2xtorsion: cannot create 2xtorsion_gb.RST: Permission denied ./Run.nmropt_1_2xtorsion: 50: ./Run.nmropt_1_2xtorsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1_2xtorsion: Program error Makefile:25: recipe for target 'pmemd_incompat_gb' failed make[3]: [pmemd_incompat_gb] Error 1 (ignored) cd pme/2xangle && ./Run.nmropt_1_2xangle_pbc ./Run.nmropt_1_2xangle_pbc: 17: ./Run.nmropt_1_2xangle_pbc: cannot create mdin: Permission denied ./Run.nmropt_1_2xangle_pbc: 36: ./Run.nmropt_1_2xangle_pbc: cannot create 2xangle_pbc.RST: Permission denied ./Run.nmropt_1_2xangle_pbc: 44: ./Run.nmropt_1_2xangle_pbc: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1_2xangle_pbc: Program error Makefile:46: recipe for target 'pmemd_incompat_pme' failed make[3]: [pmemd_incompat_pme] Error 1 (ignored) cd pme/jar_comtorsion && ./Run.jar_comtorsion ./Run.jar_comtorsion: 17: ./Run.jar_comtorsion: cannot create mdin: Permission denied ./Run.jar_comtorsion: 37: ./Run.jar_comtorsion: cannot create jartorsion_com_pbc.RST: Permission denied ./Run.jar_comtorsion: 47: ./Run.jar_comtorsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_comtorsion: Program error Makefile:46: recipe for target 'pmemd_incompat_pme' failed make[3]: [pmemd_incompat_pme] Error 1 (ignored) cd pme/jar_lcod && ./Run.jar_lcod ./Run.jar_lcod: 17: ./Run.jar_lcod: cannot create mdin: Permission denied ./Run.jar_lcod: 38: ./Run.jar_lcod: cannot create lcod.RST: Permission denied ./Run.jar_lcod: 45: ./Run.jar_lcod: /home/xxr/amber20/amber20///bin/sander: not found ./Run.jar_lcod: Program error Makefile:46: recipe for target 'pmemd_incompat_pme' failed make[3]: [pmemd_incompat_pme] Error 1 (ignored) cd pme/jar_lcod_dist && ./Run.lcod_dist ./Run.lcod_dist: 17: ./Run.lcod_dist: cannot create mdin: Permission denied ./Run.lcod_dist: 38: ./Run.lcod_dist: cannot create lcod.RST: Permission denied ./Run.lcod_dist: 48: ./Run.lcod_dist: /home/xxr/amber20/amber20///bin/sander: not found ./Run.lcod_dist: Program error Makefile:46: recipe for target 'pmemd_incompat_pme' failed make[3]: [pmemd_incompat_pme] Error 1 (ignored) cd pme/lcod && ./Run.lcod_pme ./Run.lcod_pme: 17: ./Run.lcod_pme: cannot create mdin: Permission denied ./Run.lcod_pme: 37: ./Run.lcod_pme: cannot create lcod.RST: Permission denied ./Run.lcod_pme: 43: ./Run.lcod_pme: /home/xxr/amber20/amber20///bin/sander: not found ./Run.lcod_pme: Program error Makefile:46: recipe for target 'pmemd_incompat_pme' failed make[3]: [pmemd_incompat_pme] Error 1 (ignored) cd pme/lcod_com && ./Run.lcod_com ./Run.lcod_com: 17: ./Run.lcod_com: cannot create mdin: Permission denied ./Run.lcod_com: 37: ./Run.lcod_com: cannot create lcod.RST: Permission denied ./Run.lcod_com: 47: ./Run.lcod_com: /home/xxr/amber20/amber20///bin/sander: not found ./Run.lcod_com: Program error Makefile:46: recipe for target 'pmemd_incompat_pme' failed make[3]: [pmemd_incompat_pme] Error 1 (ignored) cd pme/nmropt_1_2xtorsion && ./Run.nmropt_1_2xtorsion ./Run.nmropt_1_2xtorsion: 17: ./Run.nmropt_1_2xtorsion: cannot create mdin: Permission denied ./Run.nmropt_1_2xtorsion: 36: ./Run.nmropt_1_2xtorsion: cannot create 2xtorsion_pbc.RST: Permission denied ./Run.nmropt_1_2xtorsion: 50: ./Run.nmropt_1_2xtorsion: /home/xxr/amber20/amber20///bin/sander: not found ./Run.nmropt_1_2xtorsion: Program error Makefile:46: recipe for target 'pmemd_incompat_pme' failed make[3]: [pmemd_incompat_pme] Error 1 (ignored) make[3]: Leaving directory '/home/xxr/amber/amber20/test/nmropt' cd lj_12-6-4 && ./Run.12-6-4 mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.12-6-4: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd baroscalingdir && ./Run.baroscalingdir_z-dir mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.baroscalingdir_z-dir: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd ff19SB && ./Run.sander mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.sander: Program error Makefile:137: recipe for target 'test.sander.BASIC' failed make[2]: [test.sander.BASIC] Error 1 (ignored) cd gb_rna && ./Run.gbrna gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.gbrna: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gb_rna && ./Run.gbrna.min gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.gbrna.min: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gb_rna && ./Run.gbrna.ln gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.gbrna.ln: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gbsa_xfin && ./Run.gbsa1 gbsain: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.gbsa1: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd circ_dna && ./Run.circdna gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.circdna: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gb2_trx && ./Run.trxox gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.trxox: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gb7_trx && ./Run.trxox && ./Run.trxox prmtop_an gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.trxox: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gb7_trx && ./Run.trxox_md gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.trxox_md: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gb8_trx && ./Run.trxox gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.trxox: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gb8_trx && ./Run.trxox_md && ./Run.trxox_md prmtop_an gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.trxox_md: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gbneck2nu/1hji && ./Run.1hji_md gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.1hji_md: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd gbneck2nu/modified_nu/3p4a/ && ./Run.3p4a gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.3p4a: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd alpb_trx && ./Run.trxox gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.trxox: Program error Makefile:230: recipe for target 'test.sander.GB' failed make[2]: [test.sander.GB] Error 1 (ignored) cd LES_noPME && ./Run.LESmd SANDER: LES MD gas phase touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.LESmd: Program error Makefile:410: recipe for target 'test.sander.LES' failed make[2]: [test.sander.LES] Error 1 (ignored) cd LES_noPME && ./Run.LESmd.rdiel SANDER: LES MD gas phase rdiel touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.LESmd.rdiel: Program error Makefile:410: recipe for target 'test.sander.LES' failed make[2]: [test.sander.LES] Error 1 (ignored) cd LES && ./Run.PME_LES ADDLES and SANDER.LES test: addles: output_addles: Permission denied. At line 71 of file /home/xxr/amber20/amber20_src/AmberTools/src/addles/of.F (unit = 28) Fortran runtime error: Cannot open file 'LES.prmtop': Permission denied Error termination. Backtrace: #0 0x145c3e7e232a #1 0x145c3e7e2ed5 #2 0x145c3e7e369d #3 0x145c3e955ecd #4 0x145c3e956214 #5 0x56528c499aa5 #6 0x56528c47386f #7 0x56528c47cf42 #8 0x145c3e3f7b96 #9 0x56528c473089 #10 0xffffffffffffffff ./Run.PME_LES: Program error Makefile:410: recipe for target 'test.sander.LES' failed make[2]: [test.sander.LES] Error 1 (ignored) cd LES_CUT && ./Run.LES SANDER.LES test, no PME /home/xxr/amber20/amber20///bin/sander.LES: Command not found. ./Run.LES: Program error Makefile:410: recipe for target 'test.sander.LES' failed make[2]: [test.sander.LES] Error 1 (ignored) cd LES_TEMP && ./Run.2temp SANDER: LES T coupling touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.2temp: Program error Makefile:410: recipe for target 'test.sander.LES' failed make[2]: [test.sander.LES] Error 1 (ignored) cd LES_GB && ./Run.LES SANDER: LES+GB touch: cannot touch 'dummy': Permission denied 1: GB/LES GB1 diffcoords dummy: No such file or directory. ./Run.LES: Program error Makefile:410: recipe for target 'test.sander.LES' failed make[2]: [test.sander.LES] Error 1 (ignored) cd PIMD/part_pimd_water && ./Run.pimd addles.out: Permission denied. possible FAILURE: file addles.out does not exist. ============================================================== pimd.in: Permission denied. /home/xxr/amber20/amber20///bin/sander.LES: Command not found. ./Run.pimd: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd PIMD/part_nmpimd_water && ./Run.nmpimd addles.out: Permission denied. nmpimd.in: Permission denied. /home/xxr/amber20/amber20///bin/sander.LES: Command not found. ./Run.nmpimd: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd PIMD/part_pimd_helium && ./Run.pimd pimd.in: Permission denied. /home/xxr/amber20/amber20///bin/sander.LES: Command not found. ./Run.pimd: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd PIMD/part_nmpimd_helium && ./Run.nmpimd nmpimd.in: Permission denied. /home/xxr/amber20/amber20///bin/sander.LES: Command not found. ./Run.nmpimd: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd PIMD/part_nmpimd_ntp && ./Run.nmpimd /home/xxr/amber20/amber20///bin/sander.LES: Command not found. ./Run.nmpimd: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd PIMD/part_pimd_spcfw && ./Run.pimd addles.newout: Permission denied. ./Run.pimd: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd PIMD/part_rpmd_water && ./Run.rpmd .out: Permission denied. ./Run.rpmd: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd ti_mass/pent_LES_PIMD && ./Run.pentadiene addles.out: Permission denied. /home/xxr/amber20/amber20///bin/sander.LES: Command not found. ./Run.pentadiene: Program error Makefile:765: recipe for target 'test.sander.PIMD.partial' failed make[2]: [test.sander.PIMD.partial] Error 1 (ignored) cd nfe && ./run-serial.sh >>>>>>> doing 'abmd_ANALYSIS' >>>>>>> doing 'abmd_FLOODING' >>>>>>> doing 'abmd_UMBRELLA' >>>>>>> doing 'smd' ** Error ** : '/home/xxr/amber20/amber20///bin/sander' is not executable >>>>>>> doing 'pmd' ** Error ** : '/home/xxr/amber20/amber20///bin/sander' is not executable >>>>>>> doing 'smd2' ** Error ** : '/home/xxr/amber20/amber20///bin/sander' is not executable cd sander_pbsa_dmp && ./Run.dmp.min ./Run.dmp.min: 21: ./Run.dmp.min: cannot create min.in: Permission denied ./Run.dmp.min: 34: ./Run.dmp.min: /home/xxr/amber20/amber20///bin/sander: not found ./Run.dmp.min: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_ipb2 && ./Run.110D.min mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.110D.min: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_delphi && ./Run.1az6.min mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.1az6.min: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_lpb && ./Run.lsolver.min min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lsolver.min: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_radi && ./Run.ion.min mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.ion.min: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_tsr && ./Run.tsrb.min mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.tsrb.min: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_frc && ./test dbf_0.argasp min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.argasp.min: Program error dbf_0.dadt min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dadt.min: Program error dbf_0.dgdc min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dgdc.min: Program error dbf_0.lysasp min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysasp.min: Program error dbf_0.polyALA min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyALA.min: Program error dbf_0.polyAT min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyAT.min: Program error dbf_1.argasp min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.argasp.min: Program error dbf_1.dadt min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dadt.min: Program error dbf_1.dgdc min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dgdc.min: Program error dbf_1.lysasp min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysasp.min: Program error dbf_1.polyALA min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyALA.min: Program error dbf_1.polyAT min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyAT.min: Program error dbf_2.argasp min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.argasp.min: Program error dbf_2.dadt min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dadt.min: Program error dbf_2.dgdc min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dgdc.min: Program error dbf_2.lysasp min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysasp.min: Program error dbf_2.polyALA min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyALA.min: Program error dbf_2.polyAT min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.polyAT.min: Program error dbf_4.420D min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.420D.min: Program error dbf_4.1F81 min.in: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1F81.min: Program error cd sander_pbsa_decres && ./Run.pbsa_decres mdin: Permission denied. Error opening unit 6: File "mdout.pbsa_decres" exists (use -O to overwrite) ./Run.pbsa_decres: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_decpw && ./Run.pbsa_decpw mdin: Permission denied. Error opening unit 6: File "mdout.pbsa_decpw" exists (use -O to overwrite) ./Run.pbsa_decpw: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_ligand && ./Run ./Run: 19: ./Run: cannot create min.in: Permission denied ./Run: 37: ./Run: /home/xxr/amber20/amber20///bin/sander: not found ./Run: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd sander_pbsa_imin5 && ./Run.min mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.min: Program error Makefile:1579: recipe for target 'test.pbsa' failed make[2]: [test.pbsa] Error 1 (ignored) cd cnstph/implicit && ./Run.cnstph ./Run.cnstph: 26: ./Run.cnstph: cannot create mdin: Permission denied ./Run.cnstph: 43: ./Run.cnstph: /home/xxr/amber20/amber20///bin/sander: not found ./Run.cnstph: Program error Makefile:296: recipe for target 'test.sander.constph' failed make[2]: *** [test.sander.constph] Error 1 cd cnste/implicit && ./Run.cnste ./Run.cnste: 26: ./Run.cnste: cannot create mdin: Permission denied ./Run.cnste: 43: ./Run.cnste: /home/xxr/amber20/amber20///bin/sander: not found ./Run.cnste: Program error Makefile:300: recipe for target 'test.sander.conste' failed make[2]: *** [test.sander.conste] Error 1 cd cnstphe/implicit && ./Run.cnstphe ./Run.cnstphe: 26: ./Run.cnstphe: cannot create mdin: Permission denied ./Run.cnstphe: 44: ./Run.cnstphe: /home/xxr/amber20/amber20///bin/sander: not found ./Run.cnstphe: Program error Makefile:304: recipe for target 'test.sander.constphe' failed make[2]: *** [test.sander.constphe] Error 1 cd rism3d/ala && ./Run.ala touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.mdiis0 touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.mdiis1 touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.dist touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.dist.xyzv touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.hnc touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.list touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.imin5 touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.resize.fast touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.tree.fast touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.nacl.fast touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.nacl.tree.fast touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/ala && ./Run.ala.min.fast touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/phosphate && ./Run.ph1 touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/phosphate && ./Run.ph1.pse3 touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/phosphate && ./Run.ph1-nacl touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/phosphate && ./Run.ph1-nacl.pse3 touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/1ahoa && ./Run.1ahoa.pme SANDER: 3D-RISM: PME potential - orthorhombic touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. cd rism3d/4lzt && ./Run.4lzt.pme SANDER: 3D-RISM: PME potential - triclinic touch: cannot touch 'foo': Permission denied /home/xxr/amber20/amber20///bin/sander is not an executable or does not exist. (cd crg_reloc/water && ./Run.water.min) /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.water.min: Program error Makefile:1052: recipe for target 'test.sander.crgreloc' failed make[2]: [test.sander.crgreloc] Error 1 (ignored) (cd crg_reloc/water && ./Run.water.md) /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.water.md: Program error Makefile:1052: recipe for target 'test.sander.crgreloc' failed make[2]: [test.sander.crgreloc] Error 1 (ignored) cd amd && make -k test make[3]: Entering directory '/home/xxr/amber/amber20/test/amd' Testing AMD with PME gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pme.amd1: Program error Makefile:6: recipe for target 'pme' failed make[3]: [pme] Error 1 (ignored) gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pme.amd2: Program error Makefile:6: recipe for target 'pme' failed make[3]: [pme] Error 1 (ignored) gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.pme.amd3: Program error Makefile:6: recipe for target 'pme' failed make[3]: [pme] Error 1 (ignored) Testing AMD with GB gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.gb.amd1: Program error Makefile:18: recipe for target 'gb' failed make[3]: [gb] Error 1 (ignored) gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.gb.amd2: Program error Makefile:18: recipe for target 'gb' failed make[3]: [gb] Error 1 (ignored) gbin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.gb.amd3: Program error Makefile:18: recipe for target 'gb' failed make[3]: [gb] Error 1 (ignored) make[3]: Leaving directory '/home/xxr/amber/amber20/test/amd' cd scaledMD && make -k test make[3]: Entering directory '/home/xxr/amber/amber20/test/scaledMD' Testing scaledMD with PME mdin: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. ./Run.scaledMD: Program error Makefile:6: recipe for target 'pme' failed make[3]: *** [pme] Error 1 make[3]: Target 'test' not remade because of errors. make[3]: Leaving directory '/home/xxr/amber/amber20/test/scaledMD' Makefile:928: recipe for target 'test.serial.sander.AMD' failed make[2]: [test.serial.sander.AMD] Error 2 (ignored) export TESTsander='/sander'; cd gb_rna && ./Run.gbrna.sgld gbin: Permission denied. /sander: Command not found. ./Run.gbrna.sgld: Program error Makefile:1193: recipe for target 'test.serial.sander.sgld' failed make[2]: [test.serial.sander.sgld] Error 1 (ignored) export TESTsander='/sander'; cd gb_rna && ./Run.gbrna.sgldfp gbin: Permission denied. /sander: Command not found. ./Run.gbrna.sgldfp: Program error Makefile:1193: recipe for target 'test.serial.sander.sgld' failed make[2]: [test.serial.sander.sgld] Error 1 (ignored) export TESTsander='/sander'; cd gb_rna && ./Run.gbrna.sgldg gbin: Permission denied. /sander: Command not found. ./Run.gbrna.sgldg: Program error Makefile:1193: recipe for target 'test.serial.sander.sgld' failed make[2]: [test.serial.sander.sgld] Error 1 (ignored) export TESTsander='/sander'; cd gb_rna && ./Run.gbrna.sgmdg gbin: Permission denied. /sander: Command not found. ./Run.gbrna.sgmdg: Program error Makefile:1193: recipe for target 'test.serial.sander.sgld' failed make[2]: [test.serial.sander.sgld] Error 1 (ignored) export TESTsander='/sander'; cd emap/ && ./Run.emap emapin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.emap: Program error Makefile:1537: recipe for target 'test.serial.sander.emap' failed make[2]: [test.serial.sander.emap] Error 1 (ignored) export TESTsander='/sander'; cd emap2/ && ./Run.emap2 mmlv.in: Permission denied. /home/xxr/amber20/amber20///bin/sander: Command not found. possible FAILURE: (ignored) file emap2.out does not exist. ============================================================== possible FAILURE: (ignored) file emap2.x does not exist. ============================================================== export TESTsander=/sander; cd sander_OIN && ./Run.sander.OIN gbin: Permission denied. /sander: Command not found. ./Run.sander.OIN: Program error Makefile:838: recipe for target 'test.sander.OIN' failed make[2]: [test.sander.OIN] Error 1 (ignored) cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.min mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_charmm.min: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) cd chamber/md_engine/dhfr && ./Run.dhfr_charmm.md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_charmm.md: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.min mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_charmm.min: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) cd chamber/md_engine/dhfr_cmap && ./Run.dhfr_charmm.md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_charmm.md: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.min mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_cmap_pbc_charmm_noshake.min: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm_noshake.md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_cmap_pbc_charmm_noshake.md: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.min mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_cmap_pbc_charmm.min: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) cd chamber/md_engine/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_charmm.md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.dhfr_cmap_pbc_charmm.md: Program error Makefile:335: recipe for target 'test.sander.CHARMM' failed make[2]: [test.sander.CHARMM] Error 1 (ignored) export TESTsander=/sander; cd sinr && ./RUN.sander.SINR gbin: Permission denied. cp: cannot create regular file 'sinrvels.rst': Permission denied /sander: Command not found. ./RUN.sander.SINR: Program error Makefile:844: recipe for target 'test.sander.SINR' failed make[2]: [test.sander.SINR] Error 1 (ignored) export TESTsander=/sander; cd sander_music/ptsurf-12h2o && ./Run.music-energy touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.music-energy: Program error Makefile:850: recipe for target 'test.sander.music' failed make[2]: [test.sander.music] Error 1 (ignored) export TESTsander=/sander; cd sander_music/pt-water-gal17 && ./Run.md touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.md: Program error Makefile:850: recipe for target 'test.sander.music' failed make[2]: [test.sander.music] Error 1 (ignored) export TESTsander=/sander; cd sander_music/pt-water-vsgal17 && ./Run.md touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.md: Program error Makefile:850: recipe for target 'test.sander.music' failed make[2]: [test.sander.music] Error 1 (ignored) cd middle-scheme/MD_Unconstr_Langevin_water && ./Run.LGV_LF AMBERHOME is /home/xxr/amber20/amber20// No such file: /home/xxr/amber20/amber20///bin/sander cd middle-scheme/MD_Constr_Langevin_water && ./Run.LGV_LF AMBERHOME is /home/xxr/amber20/amber20// No such file: /home/xxr/amber20/amber20///bin/sander cd middle-scheme/QMMM_Constr_ALA_Methol && ./Run.qmmm No such file: /home/xxr/amber20/amber20///bin/sander cd nmode && ./Run.ala-dipeptide NMODE: find normal modes /home/xxr/amber20/amber20///bin/nmode: Command not found. ./Run.ala-dipeptide: Program error Makefile:1574: recipe for target 'test.nmode' failed make[2]: [test.nmode] Error 1 (ignored) cd nmode && ./Run.ala-dipeptide_rgroup NMODE: find normal modes, with a restraint weighting /home/xxr/amber20/amber20///bin/nmode: Command not found. ./Run.ala-dipeptide_rgroup: Program error Makefile:1574: recipe for target 'test.nmode' failed make[2]: [test.nmode] Error 1 (ignored) cd newton_raph && ./Run.newton_raph Unit 6 Error on OPEN: nmd_min.out ./Run.newton_raph: Program error Makefile:1574: recipe for target 'test.nmode' failed make[2]: [test.nmode] Error 1 (ignored) cd qmmm2/input_validation && ./Run.invalid_atom_ids mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.invalid_atom_ids: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/input_validation && ./Run.non_unique_qm_atoms mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.non_unique_qm_atoms: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_0 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_diag_routine_0: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_diag_routine_2: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_3 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_diag_routine_3: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_4 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_diag_routine_4: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_5 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_diag_routine_5: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_6 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_diag_routine_6: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_diag_routine_7 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_diag_routine_7: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb0 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb0: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb1 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb1: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb2: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb2_saltcon mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb2_saltcon: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.nma_md_qmgb3 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb3: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD && ./Run.C6H4FCL_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.C6H4FCL_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_shake && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_tight_p && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_tight_p && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGPM3 && ./Run.C6H4FCL_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.C6H4FCL_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGPM3_08 && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGPM3_08 && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PDDGMNDO && ./Run.C6H4FCL_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.C6H4FCL_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_AM1 && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_AM1 && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_AM1 && ./Run.C6H4FCL_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.C6H4FCL_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_AM1_ADDMM && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_AM1_ADDMM && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_RM1 && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_RM1 && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_RM1 && ./Run.C6H4FCL_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.C6H4FCL_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_MNDO && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_MNDO && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_MNDO && ./Run.C6H4FCL_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.C6H4FCL_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PM6 && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_PM6 && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb0 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb0: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb2: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/pure_QM_MD_NUMER_DERIV && ./Run.nma_md_qmgb2_saltcon mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_qmgb2_saltcon: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/1-2-ethanediol_PM3CARB1 && ./Run.PM3CARB1_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.PM3CARB1_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3 && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3 && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3 && ./Run.lysine_md_qmmm_int0 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_qmmm_int0: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3 && ./Run.lysine_md_qmmm_int2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_qmmm_int2: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3 && ./Run.lysine_md_lnk_dis_neg mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_lnk_dis_neg: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3 && ./Run.lysine_md_lnk_method2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_lnk_method2: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb0 && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb0 && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_igb2: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb5 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_igb5: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_igb7 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_igb7: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_adjust_q1 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_adjust_q1: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_adjust_q2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_adjust_q2: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2 && ./Run.lysine_md_lnk_dis_neg mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md_lnk_dis_neg: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_qmgb2_alpb && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_calc_mulliken && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_calc_mulliken && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM3_calc_dipole && ./Run.lysine_qmmm mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_qmmm: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_AM1 && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_AM1 && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_MNDO && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_MNDO && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM6 && ./Run.lysine mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/lysine_PM6 && ./Run.lysine_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.lysine_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/meoh-nh3_PM6-DH+ && ./Run.meoh-nh3 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.meoh-nh3: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/meoh-nh3_PM6-DH+ && ./Run.meoh-nh3_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.meoh-nh3_md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/PM3-MMX && ./Run.water_dimer.x mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.water_dimer.x: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/PM3-MMX && ./Run.ammonia_dimer.x mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.ammonia_dimer.x: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/PM3-MMX && ./Run.formic_acid_dimer.x mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.formic_acid_dimer.x: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/PM3-MMX2 && ./Run.water_dimer.x mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.water_dimer.x: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/PM3-MMX2 && ./Run.ammonia_dimer.x mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.ammonia_dimer.x: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/PM3-MMX2 && ./Run.formic_acid_dimer.x mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.formic_acid_dimer.x: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/PM3-MMX2 && ./Run.methanethiol.x mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.methanethiol.x: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/znme2/ && ./Run.min touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.min: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/znme2/ && ./Run.md touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/cysdip/ && ./Run.mndod.min touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.mndod.min: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/cysdip/ && ./Run.mndod.md touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.mndod.md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/cysdip/ && ./Run.mndod-mm.min touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.mndod-mm.min: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/cysdip/ && ./Run.mndod-mm.md touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.mndod-mm.md: Program error Makefile:428: recipe for target 'test.sander.QMMM.nopar' failed make[2]: [test.sander.QMMM.nopar] Error 1 (ignored) cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_imaged mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.oct_nma_imaged: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/xcrd_build_test/ && ./Run.oct_nma_noimage mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.oct_nma_noimage: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.ortho_qmewald0: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/xcrd_build_test/ && ./Run.truncoct_qmewald0 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.truncoct_qmewald0: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin_md_calc_mulliken mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_calc_mulliken: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_qmgb2: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_alpb mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_qmgb2_alpb: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq1 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_qmgb2_aq1: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_aq2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_qmgb2_aq2: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_2 && ./Run.crambin_md_qmgb2_saltcon mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_qmgb2_saltcon: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_internal mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_internal: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspev mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_dspev: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevd mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_dspevd: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dspevx mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_dspevx: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyev mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_dsyev: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevd mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_dsyevd: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_dsyevr mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_dsyevr: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_test_diagonalizers && ./Run.1NLN_auto mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_auto: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_min mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_min: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq1 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_aq1: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_aq2: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_mmcorr mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_mmcorr: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_qmewald2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_qmewald2: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb2: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_aq2_NUMER_DERIV mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_aq2_NUMER_DERIV: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_dis_neg mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_lnk_dis_neg: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/1NLN_periodic_lnk_atoms && ./Run.1NLN_MD_ntb1_lnk_method2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_lnk_method2: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.notimaged: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.notimaged_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.notimaged_md_pme: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.notimaged_md_pme_qmewald: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.notimaged_md_pme_qmewald_lowmem mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.notimaged_md_pme_qmewald_lowmem: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.imaged: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.imaged_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.imaged_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.img_center: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.img_center_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_periodic && ./Run.img_center_bigqmcut_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.img_center_bigqmcut_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin && ./Run.crambin mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin && ./Run.crambin_md_hot_start mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_hot_start: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin && ./Run.crambin_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/tip3p_cap && ./Run.tip3p_cap mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip3p_cap: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip3p_cap_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip3p_cap_md.shake: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/tip3p_cap && ./Run.tip3p_cap_md.shake_qmshakeoff mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.tip3p_cap_md.shake_qmshakeoff: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.MG_QM_water_MM: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_qmcut && ./Run.MG_QM_water_MM_MD mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.MG_QM_water_MM_MD: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_qmcut_lowmem && ./Run.MG_QM_water_MM_MD mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.MG_QM_water_MM_MD: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.MG_QM_water_MM: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MG_QM_water_MM_AM1_qmcut_ADDMM && ./Run.MG_QM_water_MM_MD mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.MG_QM_water_MM_MD: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/variable_solvent && ./Run.mg_periodic_vsolv_wat mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.mg_periodic_vsolv_wat: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/variable_solvent && ./Run.1NLN_MD_ntb1_vsolv mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.1NLN_MD_ntb1_vsolv: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/PM3-MMX && ./Run.crambin_md_pm3mmx mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_pm3mmx: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/PM3-MMX2 && ./Run.crambin_md_pm3mmx2 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md_pm3mmx2: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_PM6 && ./Run.crambin mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/crambin_PM6 && ./Run.crambin_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.crambin_md: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/PM3-MAIS && ./Run.zundel mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.zundel: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/PM3-MAIS && ./Run.hcl_wat mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.hcl_wat: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_PDDGPM3 mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.MechEm_PDDGPM3: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm2/qmmm_switching_func && ./Run.nma_md_switching mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma_md_switching: Program error Makefile:520: recipe for target 'test.sander.QMMM' failed make[2]: [test.sander.QMMM] Error 1 (ignored) cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb0 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_md_qmgb2_saltcon DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_DFTB && ./Run.nma_disp DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_shake_DFTB && ./Run.nma_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/pure_QM_MD_tight_p_DFTB && ./Run.nma_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_dis_neg DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_lnk_method2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB && ./Run.lysine_md_qmmm_int0 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb0 && ./Run.lysine_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb5 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_igb7 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2 && ./Run.lysine_md_adjust_q2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_qmgb2_alpb && ./Run.lysine_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/lysine_DFTB_calc_mulliken && ./Run.lysine_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/3rd-order/water && ./Run.water DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/3rd-order/water && ./Run.water_read_mdin DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/3rd-order/water && ./Run.water_read_file DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/dftb3/water && ./Run.h2o.go DFTB3 3ob-3-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/dftb3/water && ./Run.h2o.md DFTB3 3ob-3-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md_hot_start DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_DFTB && ./Run.crambin_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_calc_mulliken DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_alpb DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_aq2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/crambin_2_DFTB && ./Run.crambin_md_qmgb2_saltcon DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_link_atoms DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb1_qmewald2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_ewald_ntb2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_link_atoms_aq2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_qmewald2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/aladip_tip3p_ewaldpme && ./Run.aladip_pme_ntb2_telec DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut && ./Run.MG_QM_water_MM_MD DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.notimaged_md_pme_qmewald DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.imaged_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_periodic && ./Run.img_center_bigqmcut_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/MG_QM_water_MM_DFTB_qmcut_lowmem && ./Run.MG_QM_water_MM_MD DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/tip3p_cap_DFTB && ./Run.tip3p_cap_md.shake_qmshakeoff DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_min DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_dis_neg DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_lnk_method2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq1_disp DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_aq2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb1_qmewald2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB && ./Run.1NLN_MD_ntb2 DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PA DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/3rd-order/ala8 && ./Run.ala8_PR DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm2/MechEm_nma-spcfwbox && ./Run.MechEm_DFTB DFTB2 mio-1-1 SLKO files not found - Skipping DFTB tests... cd qmmm_DFTB/dftb3/nma-h2o-box && ./Run.nma-spcfw-15.md DFTB3 3ob-3-1 SLKO files not found - Skipping DFTB tests... cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF dftb executable is called dftb.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.dftb_md ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF dftb executable is called dftb.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.lda-sz_md ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_ADF && ./Run.h2o.template.lda-sz ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.bp86_6-31g_md GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_GAMESS && ./Run.h2o.template.bp86_6-31g GAMESS not installed - Skipping Test... Check your GAMESS installation and make sure that the GAMESS executable is called rungms cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.blyp_6-31g_md TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_TeraChem && ./Run.h2o.template.blyp_6-31g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g GAUSSIAN will run on 1 CPU core (environment variable GAU_NCPUS not set) mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.h2o.blyp_sto-3g: Program error Makefile:698: recipe for target 'test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 1 (ignored) cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.blyp_sto-3g_md GAUSSIAN will run on 1 CPU core (environment variable GAU_NCPUS not set) mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.h2o.blyp_sto-3g_md: Program error Makefile:698: recipe for target 'test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 1 (ignored) cd qmmm_EXTERN/pure_QM_MD_GAUSSIAN && ./Run.h2o.template.blyp_sto-3g GAUSSIAN will run on 1 CPU core (environment variable GAU_NCPUS not set) mdin: Permission denied. cp: cannot create regular file 'gau_job.tpl': Permission denied touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.h2o.template.blyp_sto-3g: Program error Makefile:698: recipe for target 'test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 1 (ignored) cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.blyp_6-31g_md Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_Orca && ./Run.h2o.template.blyp_6-31g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/pure_QM_MD_NWChem && ./Run.h2o.blyp_sto-3g_md NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.template.blyp_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_Q-Chem && ./Run.h2o.blyp_6-31g_md Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/pure_QM_MD_MRCC && ./Run.h2o.hf_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_MRCC && ./Run.h2o.template.blyp_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/pure_QM_MD_MRCC && ./Run.h2o.blyp_6-31g_md MRCC not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_ADF && ./Run.aladip.blyp_dz.MechEm ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/QMMM_MD_ADF && ./Run.nma-spcfw-15.blyp_dz.MechEm ADF not installed - Skipping Test... Check your ADF installation and make sure that the ADF executable is called adf.exe cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.aladip.hf_sto-3g.MechEm Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_Orca && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Orca not installed - Skipping Test... Check your Orca installation and make sure that the Orca executable is called orca cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.aladip.hf_sto-3g.MechEm TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_TeraChem && ./Run.nma-spcfw-15.hf_sto-3g.MechEm TeraChem not installed - Skipping Test... Check your TeraChem installation and make sure that the TeraChem executable is called terachem cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.aladip.hf_sto-3g GAUSSIAN will run on 1 CPU core (environment variable GAU_NCPUS not set) mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.aladip.hf_sto-3g: Program error Makefile:698: recipe for target 'test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 1 (ignored) cd qmmm_EXTERN/QMMM_MD_GAUSSIAN && ./Run.nma-spcfw-15.hf_sto-3g GAUSSIAN will run on 1 CPU core (environment variable GAU_NCPUS not set) mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.nma-spcfw-15.hf_sto-3g: Program error Makefile:698: recipe for target 'test.sander.EXTERN' failed make[2]: [test.sander.EXTERN] Error 1 (ignored) cd qmmm_EXTERN/QMMM_MD_NWChem && ./Run.aladip.hf_sto-3g NWChem not installed - Skipping Test... Check your NWChem installation and make sure that the NWChem executable is called nwchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.aladip.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.aladip.hf_sto-3g.MechEm Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.nma-spcfw-15.hf_sto-3g Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_Q-Chem && ./Run.nma-spcfw-15.hf_sto-3g.MechEm Q-Chem not installed - Skipping Test... Check your Q-Chem installation and make sure that the Q-Chem executable is called qchem cd qmmm_EXTERN/QMMM_MD_MRCC && ./Run.aladip.hf_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/QMMM_MD_MRCC && ./Run.nma-spcfw-15.hf_sto-3g MRCC not installed - Skipping Test... cd qmmm_EXTERN/QMMM_Lio/water && ./Run.water Lio is not installed - Skipping Test... Check your Lio installation and the LIOHOME environment setting cd qmmm_EXTERN/QMMM_Lio/water && ./Run.td.water Lio is not installed - Skipping Test... Check your Lio installation and the LIOHOME environment setting cd qmmm_EXTERN/QMMM_Fireball/min && ./Run.min Not compiled with Fireball - Skipping Test... cd qmmm_EXTERN/QMMM_Fireball/md && ./Run.md Not compiled with Fireball - Skipping Test... cd abfqmmm/abfqmmm_water_sp && ./Run.abfqmmm_water_sp mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.abfqmmm_water_sp: Program error Makefile:687: recipe for target 'test.sander.ABFQMMM' failed make[2]: [test.sander.ABFQMMM] Error 1 (ignored) cd abfqmmm/abfqmmm_water_md && ./Run.abfqmmm_water_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.abfqmmm_water_md: Program error Makefile:687: recipe for target 'test.sander.ABFQMMM' failed make[2]: [test.sander.ABFQMMM] Error 1 (ignored) cd abfqmmm/abfqmmm_dmpoh_md && ./Run.abfqmmm_dmpoh_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.abfqmmm_dmpoh_md: Program error Makefile:687: recipe for target 'test.sander.ABFQMMM' failed make[2]: [test.sander.ABFQMMM] Error 1 (ignored) cd abfqmmm/abfqmmm_lysozyme_md && ./Run.abfqmmm_lysozyme_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.abfqmmm_lysozyme_md: Program error Makefile:687: recipe for target 'test.sander.ABFQMMM' failed make[2]: [test.sander.ABFQMMM] Error 1 (ignored) cd abfqmmm/adqmmm_water_md && ./Run.adqmmm_water_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.adqmmm_water_md: Program error Makefile:687: recipe for target 'test.sander.ABFQMMM' failed make[2]: [test.sander.ABFQMMM] Error 1 (ignored) cd abfqmmm/hotspot_water_md && ./Run.hotspot_water_md mdin: Permission denied. touch: cannot touch 'dummy': Permission denied dummy: No such file or directory. ./Run.hotspot_water_md: Program error Makefile:687: recipe for target 'test.sander.ABFQMMM' failed make[2]: [test.sander.ABFQMMM] Error 1 (ignored) cd sebomd/AM1/dimethylether && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1/methionine && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1/n-methyl-acetamide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1/nucleoside && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1/water1 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1-d-PhoT/dimethylether && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1-d-PhoT/methionine && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1-d-PhoT/n-methyl-acetamide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1-d-PhoT/nucleoside && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. /home/xxr/amber20/amber20///test/dacdif: Command not found. /home/xxr/amber20/amber20///bin/sander: Command not found. /home/xxr/amber20/amber20///test/dacdif: Command not found. cd sebomd/AM1-d-PhoT/water1 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1-d-CB1/dimethylether && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1-d-CB1/n-methyl-acetamide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/AM1-d-CB1/water1 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/DC/water32 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/Ewald-CM1/Water2 && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./md.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/Ewald-ConstantCharge/Water2 && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./md.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/Ewald-Mulliken/Water2 && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./md.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/MinimumImage/Water2 && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./md.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/method3/alaninedipeptide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/method3/ethanol_and_water && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/MNDO/dimethylether && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/MNDO/methionine && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/MNDO/n-methyl-acetamide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/MNDO/nucleoside && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/MNDO/water1 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/RM1/dimethylether && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/RM1/methionine && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/RM1/n-methyl-acetamide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/RM1/nucleoside && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) # -cd sebomd/RM1/water1 && ./min.csh && ./md.csh cd sebomd/RM1/water1 && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./md.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PIF2/dimethylether && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PIF2/water1 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PIF2/doublewater && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PIF2/ethanol_and_water && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PIF3/water1 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PIF3/doublewater && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PIF3/ethanol_and_water && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PM3/alaninedipeptide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PM3/dimethylether && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PM3/methionine && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PM3/n-methyl-acetamide && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PM3/nucleoside && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) cd sebomd/PM3/water1 && ./min.csh && ./md.csh /home/xxr/amber20/amber20///bin/sander: Command not found. ./min.csh: Program error Makefile:247: recipe for target 'test.serial.sander.SEBOMD' failed make[2]: [test.serial.sander.SEBOMD] Error 1 (ignored) export TESTsander='/sander'; unset DO_PARALLEL; cd emil/emil_sander_gbsa && ./Run.emil EMIL was not configured at build time: skipping test run $AMBERHOME/configure for more information cd sanderapi && make test make[3]: Entering directory '/home/xxr/amber/amber20/test/sanderapi' Makefile:1: /home/xxr/amber20/amber20///config.h: No such file or directory make[3]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. make[3]: Failed to remake makefile '/home/xxr/amber20/amber20///config.h'. (if [ -f "/libsander" ]; then \ make test_all; \ else \ make test_none; \ fi;) make[4]: Entering directory '/home/xxr/amber/amber20/test/sanderapi' Makefile:1: /home/xxr/amber20/amber20///config.h: No such file or directory make[4]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. make[4]: Failed to remake makefile '/home/xxr/amber20/amber20///config.h'. The SANDER API was not installed. Skipping SANDER API tests. make[4]: Leaving directory '/home/xxr/amber/amber20/test/sanderapi' Makefile:4: recipe for target 'test' failed make[3]: *** [test] Error 2 make[3]: Leaving directory '/home/xxr/amber/amber20/test/sanderapi' Makefile:1532: recipe for target 'test.serial.sanderapi' failed make[2]: [test.serial.sanderapi] Error 2 (ignored) cd sanderlesapi && make test make[3]: Entering directory '/home/xxr/amber/amber20/test/sanderlesapi' Makefile:1: /home/xxr/amber20/amber20///config.h: No such file or directory make[3]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. make[3]: Failed to remake makefile '/home/xxr/amber20/amber20///config.h'. (if [ -f "/libsanderles" ]; then \ make test_all; \ else \ make test_none; \ fi;) make[4]: Entering directory '/home/xxr/amber/amber20/test/sanderlesapi' Makefile:1: /home/xxr/amber20/amber20///config.h: No such file or directory make[4]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. make[4]: Failed to remake makefile '/home/xxr/amber20/amber20///config.h'. The SANDER LES API was not installed. Skipping SANDER LES API tests. make[4]: Leaving directory '/home/xxr/amber/amber20/test/sanderlesapi' Makefile:4: recipe for target 'test' failed make[3]: *** [test] Error 2 make[3]: Leaving directory '/home/xxr/amber/amber20/test/sanderlesapi' Makefile:1532: recipe for target 'test.serial.sanderapi' failed make[2]: [test.serial.sanderapi] Error 2 (ignored) make[2]: Target 'test.serial' not remade because of errors. make[2]: Leaving directory '/home/xxr/amber/amber20/test' make[2]: Entering directory '/home/xxr/amber/amber20/test' Makefile:4: /home/xxr/amber20/amber20///config.h: No such file or directory make[2]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. make[2]: Failed to remake makefile '/home/xxr/amber20/amber20///config.h'. make[2]: *** No rule to make target 'test.gem.pmemd.', needed by 'test.serial.gem.pmemd'. make[2]: Target 'test.serial.gem.pmemd' not remade because of errors. make[2]: Leaving directory '/home/xxr/amber/amber20/test' make[2]: Entering directory '/home/xxr/amber/amber20/AmberTools/test' Makefile:2: /home/xxr/amber20/amber20///config.h: No such file or directory make[2]: *** No rule to make target '/home/xxr/amber20/amber20///config.h'. Stop. make[2]: Leaving directory '/home/xxr/amber/amber20/AmberTools/test' 0 file comparisons passed 61 file comparisons failed (2 of which can be ignored) 523 tests experienced errors Test log file saved as /home/xxr/amber20/amber20///logs/test_at_serial/2020-05-10_19-12-25.log No test diffs to save!