Hello!
I have recently started using AmberTools. Tleap is working fine for me for some things (example, radial distribution
functions), but somehow it cannot load/source some files which are part of the AmberTools distribution.
Examples:
loadOff all_nucleic94.lib
Loading library: /usr/local/amber11/dat/leap/lib/all_nucleic94.lib
Segmentation fault
I don't know if this is related with the errors I get when doing make test after installing AmberTools (log below, sorry
for the length).
Thanks a lot in advance.
Luis
make[1]: Entering directory `/usr/local/amber11/AmberTools/test'
(find antechamber -name '*.out' -o -name '*.log' -o -name '*.lib' -o \
-name "*.dif" | \
while read dif ;\
do \
rm -f $dif ;\
done ;\
)
(cd leap && /bin/rm -f *.log *.out *.lib *.top )
(cd ptraj_rmsa && /bin/rm -f *.dif )
(cd ptraj_matrix && /bin/rm -f *.dif )
(cd ptraj_rms && /bin/rm -f *.dif )
(cd ptraj_les && /bin/rm -f *.dif )
(find sleap -name '*.out' -o -name '*.log' -o -name '*.lib' -o \
-name "*.dif" | \
while read dif ;\
do \
rm -f $dif ;\
done ;\
)
(find sqm -name '*.out' -o -name '*.dif' | \
while read dif ;\
do \
rm -f $dif ;\
done ;\
)
/bin/rm -f TEST_FAILURES.diff
cd nab && make -k testlibrism
make[2]: Entering directory `/usr/local/amber11/AmberTools/test/nab'
Running test to make dna duplex:
setpoint: :C44: no atoms selected
setpoint: :C66: no atoms selected
end1/end2 in ligate() must be be 5'/3' or 3'/5 not lstt/fisst
./Run.duplex: Program error
make[2]: *** [duplex_test] Error 1
Running test to computed 3DNA deformation energies:
deform.c: In function ‘main’:
deform.c:24: warning: unknown conversion type character ‘\’ in format
diffing deform.out.check with deform.out
possible FAILURE: check deform.out.dif
==============================================================
Running Reflexive test:
reflexive.c: In function ‘main’:
reflexive.c:27: warning: unknown conversion type character 0xa in format
reflexive.c:29: warning: unknown conversion type character 0xa in format
reflexive.c:32: warning: unknown conversion type character 0xa in format
reflexive.c:35: warning: unknown conversion type character 0xa in format
reflexive.c:41: warning: unknown conversion type character 0xa in format
reflexive.c:45: warning: unknown conversion type character 0xa in format
reflexive.c:49: warning: unknown conversion type character 0xa in format
reflexive.c:53: warning: unknown conversion type character 0xa in format
reflexive.c:58: warning: unknown conversion type character 0xa in format
reflexive.c:63: warning: unknown conversion type character 0xa in format
reflexive.c:67: warning: unknown conversion type character 0xa in format
reflexive.c:71: warning: unknown conversion type character 0xa in format
reflexive.c:75: warning: unknown conversion type character 0xa in format
reflexive.c:80: warning: unknown conversion type character 0xa in format
diffing ref.out.check with ref.out
possible FAILURE: check ref.out.dif
==============================================================
Running test of hashed arrays:
hash.c: In function ‘main’:
hash.c:30: warning: unknown conversion type character 0xa in format
diffing hash.out.check with hash.out
possible FAILURE: check hash.out.dif
==============================================================
Running test to compute chemical shifts
(this tests many parts of the compiler and libraries)
shifts.c: In function ‘main’:
shifts.c:439: warning: unknown conversion type character 0xa in format
shifts.c:667: warning: unknown conversion type character 0x20 in format
shifts.c:667: warning: format ‘%8.3f’ expects type ‘double’, but argument 2 has type ‘STRING_T *’
shifts.c:690: warning: unknown conversion type character 0x9 in format
shifts.c:690: warning: format ‘%.3f’ expects type ‘double’, but argument 6 has type ‘STRING_T *’
read_obs_shifts.c: In function ‘read_obs_shifts’:
read_obs_shifts.c:89: warning: unknown conversion type character 0xa in format
swap_shifts.c: In function ‘swap_shifts’:
swap_shifts.c:46: warning: format ‘%-13s’ expects type ‘char *’, but argument 4 has type ‘REAL_T’
swap_shifts.c:46: warning: format ‘%7.3f’ expects type ‘double’, but argument 5 has type ‘STRING_T *’
write_sander_inp.c: In function ‘write_sander_inp’:
write_sander_inp.c:86: warning: unknown conversion type character 0xa in format
./Run.shifts: Program error
make[2]: *** [shifts_test] Error 1
Running test to do simple minimization
(this tests the molecular mechanics interface)
getpdb: can't open file 2.ddb
./Run.sff: Program error
make[2]: *** [sff_test] Error 1
Running test to do simple minimization with shake
(this tests the molecular mechanics interface)
getpdb: can't open file 2.ddb
./Run.shake: Program error
make[2]: *** [rattle_min_test] Error 1
Running test of fibre-diffraction module
Unable to openddata file /usrlocal/amberr11/dat/fd_daaa/anaa.att; exitin
n./Run.fd: Program error
make[2]: *** [fd_test] Error 1
Running test to do simple minimization
(this tests the generalized Born implementation)
getpdb: can't open file gbrna.ddb
./Run.gb: Program error
make[2]: *** [gb_test] Error 1
Running test to do simple minimization
(this tests the generalized Born implementation)
getpdb: can't open file xfin.dbb
./Run.xfin: Program error
make[2]: *** [xfin_test] Error 1
Running test to do simple minimization
(this tests the LCPO surface area)
getpdb: can't open file gbrna.ddb
./Run.gbsa: Program error
make[2]: *** [gbsa_test] Error 1
Running test to do simple minimization
(this tests the ao generalized Born implementation)
Error: mm_option: unknown keyword or invalid value:
first character of the option is 'g'.
./Run.gb2: Program error
make[2]: *** [gb2_test] Error 1
Running test to do molecular dynamics with rattle
getpdb: can't open file gbrna.ddb
./Run.rattle_md: Program error
make[2]: *** [rattle_md_test] Error 1
Running test of randomized embedding
setpoint: ::CC: no atoms selected
setpoint: :%::C: no atoms selected
setpoint: ::NN: no atoms selected
end1/end2 in ligate() must be be 5'/3' or 3'/5 not lstt/fisst
./Run.rembed: Program error
make[2]: *** [rembed_test] Error 1
Running test to compute NAB energy of 3dfr minus waters.
getpdb: can't open file dhrndpmtx.ambpddb
./Run.dhfrndpmtx: Program error
make[2]: *** [dhfrndpmtx_test] Error 1
Running test to compute GB Newton-Raphson and normal modes:
Error: mm_option: unknown keyword or invalid value:
first character of the option is 'c'.
./Run.asp: Program error
make[2]: *** [asp_test] Error 1
Running test to compute non-GB Newton-Raphson and normal modes:
Error: mm_option: unknown keyword or invalid value:
first character of the option is 'c'.
./Run.aspnb: Program error
make[2]: *** [aspnb_test] Error 1
Running test to create Amber force-field description
sh: /usr/local/amber11/bin/teLep: not found
getpdb: can't open file gbrna.ddb.lddb
./Run.prm: Program error
make[2]: *** [prm_test] Error 1
Running test to create a simple mmCIF file
getpdb: can't open file gbrna.ddb
./Run.cif: Program error
make[2]: *** [cif_test] Error 1
Running test to do simple xmin minimization
getpdb: can't open file gbrna.ddb
./Run.xmin: Program error
make[2]: *** [xmin_test] Error 1
Running test to do simple lmod optimization
Error: mm_option: unknown keyword or invalid value:
first character of the option is '0'.
diffing tlmod.out.check with tlmod.out
possible FAILURE: check tlmod.out.dif
==============================================================
Running test to compute GB normal modes using DSYEVD:
Error: mm_option: unknown keyword or invalid value:
first character of the option is 'c'.
./Run.nmode1: Program error
make[2]: *** [nmode1_test] Error 1
Running test to compute GB normal modes using DSAUPD:
Error: mm_option: unknown keyword or invalid value:
first character of the option is 'c'.
./Run.nmode2: Program error
make[2]: *** [nmode2_test] Error 1
Running test to compute Langevin modes:
Error: mm_option: unknown keyword or invalid value:
first character of the option is 'c'.
./Run.nmode3: Program error
make[2]: *** [nmode3_test] Error 1
Running test of the isotropic periodic sum technique
getpdb: can't open file dhfr.dbb
./Run.ips: Program error
make[2]: *** [ips_test] Error 1
Running test to do simple minimization (libpbsa)
(this tests the PBSA implementation)
getpdb: can't open file pbdmp.ddb
./Run.pbsa: Program error
make[2]: *** [pbsa_test] Error 1
Running test to do simple minimization (librism)
(this tests the 3D-RISM implementation)
rismdmp.c: In function ‘main’:
rismdmp.c:38: warning: unknown conversion type character 0xa in format
getpdb: can't open file pbdmp.ddb
./Run.rism_min: Program error
make[2]: *** [rism_test] Error 1
Running test to do basic MD (librism)
(this tests the 3D-RISM-KH implementation)
Cannot read parm file ala.pamm7
./Run.rism_md: Program error
make[2]: *** [rism_md_test] Error 1
Running test to do basic MD (librism)
(this tests the 3D-RISM-KH precission)
Cannot read parm file ala.pamm7
./Run.rism_dist: Program error
make[2]: *** [rism_dist] Error 1
Running test to do basic MD (librism)
(this tests the 3D-RISM-HNC implementation)
Cannot read parm file ala.pamm7
./Run.rism_hnc: Program error
make[2]: *** [rism_hnc] Error 1
make[2]: Target `testlibrism' not remade because of errors.
make[2]: Leaving directory `/usr/local/amber11/AmberTools/test/nab'
make[1]: *** [test.nab] Error 2
cd ptraj_rmsa && ./Run.rms
diffing rms.dat.save with rms.dat
PASSED
==============================================================
cd ptraj_rms && ./Run.rms
ptraj: test rms and 2drms commands
diffing rms_fit.dat.save with rms_fit.dat
PASSED
==============================================================
diffing rms_nofit.dat.save with rms_nofit.dat
PASSED
==============================================================
diffing rms2d.ps.save with rms2d.ps
PASSED
==============================================================
cd ptraj_matrix && ./Run.matrix
ptraj: analyze fluctuation matrices
diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat
PASSED
==============================================================
cd ptraj_order && ./Run.order
ptraj: calculate S^2 parameters and relaxation rates via IRED matrix
diffing orderparam.save with orderparam
PASSED
==============================================================
diffing noe.save with noe
PASSED
==============================================================
cd ptraj_trajectory && ./Run.ptraj
ptraj: Test processing of trajectories with offsets and compression.
diffing rem.crd.combined.save with rem.crd.combined
PASSED
==============================================================
diffing rem.crd.combined.save with gzip.rem.crd.combined
PASSED
==============================================================
diffing rem.crd.combined.save with bzip2.rem.crd.combined
PASSED
==============================================================
cd ptraj_remd_netcdf && ./Run.ptraj netcdf.mod
ptraj: Test processing of REMD trajectories.
diffing dist.crd.dat.save with dist.crd.dat
PASSED
==============================================================
ptraj: Test processing of NetCDF REMD trajectories.
diffing dist.dat.save with dist.dat
PASSED
==============================================================
cd ptraj_comprehensive && ./Run.comprehensive netcdf.mod
ptraj: Test multiple ptraj actions.
diffing dist_end_to_end.list.save with dist_end_to_end.list
PASSED
==============================================================
diffing omega.save with omega
PASSED
==============================================================
diffing phi.save with phi
PASSED
==============================================================
diffing psi.save with psi
PASSED
==============================================================
diffing watershell.list.save with watershell.list
PASSED
==============================================================
diffing test.mdcrd.save with test.mdcrd
PASSED
==============================================================
testing NetCDF...
diffing trajectory.mdcrd with trajectory_test.mdcrd
PASSED
==============================================================
cd antechamber/top2mol2 && ./Run.top2mol2
diffing sustiva.mol2.save with sustiva.mol2
PASSED
==============================================================
diffing dna.mol2.save with dna.mol2
PASSED
==============================================================
diffing dna_wat.mol2.save with dna_wat.mol2
PASSED
==============================================================
diffing aa.mol2.save with aa.mol2
PASSED
==============================================================
cd antechamber/database && ./Run.database
diffing total.frcmod.save with total.frcmod
PASSED
==============================================================
diffing total.prepi.save with total.prepi
PASSED
==============================================================
cd antechamber/bondtype && ./Run.bondtype
diffing ABAKOE.prepi.save with ABAKOE.prepi
PASSED
==============================================================
diffing PFPHHG02.prepi.save with PFPHHG02.prepi
PASSED
==============================================================
diffing fluorescein2.mol2.save with fluorescein2.mol2
PASSED
==============================================================
diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
PASSED
==============================================================
cd antechamber/c60 && ./Run.c60
diffing buckyball.mol2.save with buckyball.mol2
PASSED
==============================================================
diffing buckyball.gzmat.save with buckyball.gzmat
PASSED
==============================================================
diffing buckyball.jcrt.save with buckyball.jcrt
PASSED
==============================================================
diffing buckyball.prepi.save with buckyball.prepi
PASSED
==============================================================
diffing buckyball.ac.save with buckyball.ac
PASSED
==============================================================
cd antechamber/charmm && ./Run.charmm
diffing ala2.inp.save with ala2.inp
PASSED
==============================================================
diffing ala2.rtf.save with ala2.rtf
PASSED
==============================================================
diffing ala2.prm.save with ala2.prm
PASSED
==============================================================
diffing ala2_charmm.mol2.save with ala2_charmm.mol2
PASSED
==============================================================
cd antechamber/chemokine && ./Run.1b2t
diffing 1b2t.mol2.save with 1b2t.mol2
PASSED
==============================================================
diffing 1b2t.ac.save with 1b2t.ac
PASSED
==============================================================
cd antechamber/tp && ./Run.tp
diffing tp.mol2.save with tp.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
cd antechamber/ash && ./Run.ash
diffing ash.mol2.save with ash.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
cd antechamber/sustiva && ./Run.sustiva
diffing sustiva.mol2.save with sustiva.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
diffing leap.out.save with leap.out
PASSED
==============================================================
cd antechamber/fluorescein && ./Run.fluorescein
diffing fluorescein.mol2.save with fluorescein.mol2
PASSED
==============================================================
diffing frcmod.save with frcmod
PASSED
==============================================================
cd antechamber/guanine_amber && ./Run.guanine_amber
diffing DGN.mol2.save with DGN.mol2
PASSED
==============================================================
cd antechamber/fpph && ./Run.fpph_resp
diffing fpph_resp.mol2.save with fpph_resp.mol2
PASSED
==============================================================
cd antechamber/residuegen && ./Run.ala
diffing ala.ac.save with ala.ac
PASSED
==============================================================
diffing ala.esp.save with ala.esp
PASSED
==============================================================
diffing ala.prep.save with ala.prep
PASSED
==============================================================
cd leap && ./Run.tleap
AMBERHOME is set to /usr/local/amber11
Running leap tests on ./tleap -> ../../exe/teLeap
building force field libraries:
'91 ff..
diffing /usr/local/amber11/dat/leap/lib/all_amino91.lib with all_amino91.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/all_aminoct91.lib with all_aminoct91.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/all_aminont91.lib with all_aminont91.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/all_nucleic91.lib with all_nucleic91.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/ions91.lib with ions91.lib
PASSED
==============================================================
'94 ff..
diffing /usr/local/amber11/dat/leap/lib/all_amino94.lib with all_amino94.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/all_aminont94.lib with all_aminont94.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib
PASSED
==============================================================
diffing /usr/local/amber11/dat/leap/lib/ions94.lib with ions94.lib
PASSED
==============================================================
loadpdb and saveamberparm: 94 ff..
./Run.tleap: Program error in leap
make[1]: *** [test.leap] Error 1
cd sleap && make -k test
make[2]: Entering directory `/usr/local/amber11/AmberTools/test/sleap'
/bin/rm -f `find . -name "*.dif"`
/bin/rm -f TEST_FAILURES.diff
cd mdlsdf; ./Run.mdlsdf
diffing crown_2.sdf.save with crown_2.sdf
PASSED
==============================================================
cd tripos; ./Run.tripos
diffing wy.mol2.save with wy.mol2
PASSED
==============================================================
cd pdbent; ./Run.pdbent1
diffing 1hpv.mol2.save with 1hpv.mol2
PASSED
==============================================================
cd pdbent; ./Run.pdbent2
diffing mdl_1hpv.mol2.save with mdl_1hpv.mol2
PASSED
==============================================================
cd offlib; ./Run.off
diffing hpv.off.save with hpv.off
PASSED
==============================================================
cd source; ./Run.source
diffing source.out.save with source.out
PASSED
==============================================================
cd prmtop; ./Run.prmtop1
diffing hpv.top.save with hpv.top
PASSED
==============================================================
diffing hpv.xyz.save with hpv.xyz
PASSED
==============================================================
cd prmtop; ./Run.prmtop2
This is a long test; please wait patiently...
diffing box.out.save with box.out
PASSED
==============================================================
diffing hpv_box.top.save with hpvbox.top
PASSED
==============================================================
cd prmtop; ./Run.prmtop3
This is a long test; please wait patiently...
diffing hpv_cap.top.save with hpv_cap.top
PASSED
==============================================================
cd prmtop; ./Run.prmtoppol
diffing ubqpol.top.save with ubqpol.top
PASSED
==============================================================
diffing ubqpol.xyz.save with ubqpol.xyz
PASSED
==============================================================
cd solvate; ./Run.solvatebox
This is a long test; please wait patiently...
diffing hpvbox.pdb.save with hpvbox.pdb
PASSED
==============================================================
diffing hpvbox.top.save with hpvbox.top
PASSED
==============================================================
cd solvate; ./Run.solvatebox_closeness
This is a long test; please wait patiently...
diffing hpvbox_closeness.pdb.save with hpvbox_closeness.pdb
PASSED
==============================================================
cd solvate; ./Run.solvatecap
diffing hpvcap.pdb.save with hpvcap.pdb
PASSED
==============================================================
cd solvate; ./Run.solvateoct
This is a long test; please wait patiently...
diffing hpvoct.pdb.save with hpvoct.pdb
PASSED
==============================================================
diffing hpvoct.top.save with hpvoct.top
PASSED
==============================================================
cd solvate; ./Run.solvateshell
This is a long test; please wait patiently...
diffing hpvshell.pdb.save with hpvshell.pdb
PASSED
==============================================================
cd amoeba; ./Run.amoeba
diffing jac_2.prmtop.save with jac_2.prmtop
PASSED
==============================================================
cd amoeba; ./Run.amoeba_sol
diffing hpv.prmtop.save with hpv.prmtop
PASSED
==============================================================
cd builder; ./Run.builder
diffing water.mol2.save with water.mol2
PASSED
==============================================================
diffing wat2.mol2.save with wat2.mol2
PASSED
==============================================================
cd addions; ./Run.addions1
diffing hpv_ion.pdb.save with hpv_ion.pdb
PASSED
==============================================================
cd addions; ./Run.addions2
diffing hpv_ion2.pdb.save with hpv_ion2.pdb
PASSED
==============================================================
cd addions; ./Run.addions3
diffing 1zik_ion.mol2.save with 1zik_ion.mol2
PASSED
==============================================================
cd molinfo; ./Run.molinfo
diffing leap.out.save with leap.out
PASSED
==============================================================
cd polymer; ./Run.polymer
diffing combine.mol2.save with combine.mol2
PASSED
==============================================================
diffing sequence.mol2.save with sequence.mol2
PASSED
==============================================================
cd polymer; ./Run.impose
diffing impose.out.save with impose.out
PASSED
==============================================================
diffing impose.mol2.save with impose.mol2
PASSED
==============================================================
cd polymer; ./Run.polymer2
diffing aa.mol2.save with aa.mol2
PASSED
==============================================================
cd polymer; ./Run.zmatrix
diffing zmatrix.out.save with zmatrix.out
PASSED
==============================================================
diffing meoh.mol2.save with meoh.mol2
PASSED
==============================================================
cd bondbydis; ./Run.bondbydis
diffing wy.sdf.save with wy.sdf
PASSED
==============================================================
cd DNA; ./Run.DNA1
diffing 132d.mol2.save with 132d.mol2
PASSED
==============================================================
cd DNA; ./Run.DNA2
diffing 32d.top.save with 32d.top
PASSED
==============================================================
cd oldleap; ./Run.oldleap
diffing ff91/all_amino91.lib.save with ff91/all_amino91.lib
PASSED
==============================================================
diffing ff91/all_aminont91.lib.save with ff91/all_aminont91.lib
PASSED
==============================================================
diffing ff91/all_aminoct91.lib.save with ff91/all_aminoct91.lib
PASSED
==============================================================
diffing ff91/all_nucleic91.lib.save with ff91/all_nucleic91.lib
PASSED
==============================================================
diffing ff94/all_amino94.lib.save with ff94/all_amino94.lib
PASSED
==============================================================
diffing ff94/all_aminont94.lib.save with ff94/all_aminont94.lib
PASSED
==============================================================
diffing ff94/all_aminoct94.lib.save with ff94/all_aminoct94.lib
PASSED
==============================================================
diffing ff94/all_nucleic94.lib.save with ff94/all_nucleic94.lib
PASSED
==============================================================
diffing ff94/all_aminoan94.top.save with ff94/all_aminoan94.top
PASSED
==============================================================
diffing ff94/all_aminoan94.crd.save with ff94/all_aminoan94.crd
PASSED
==============================================================
diffing ff94/all_aminonc94.top.save with ff94/all_aminonc94.top
PASSED
==============================================================
diffing ff94/all_aminonc94.crd.save with ff94/all_aminonc94.crd
PASSED
==============================================================
diffing ff94/all_dna94.top.save with ff94/all_dna94.top
PASSED
==============================================================
diffing ff94/all_dna94.crd.save with ff94/all_dna94.crd
PASSED
==============================================================
diffing ff94/all_rna94.top.save with ff94/all_rna94.top
PASSED
==============================================================
diffing ff94/all_rna94.crd.save with ff94/all_rna94.crd
PASSED
==============================================================
cd disulfide; ./Run.auto
diffing crn.mol2.save with crn.mol2
PASSED
==============================================================
cd disulfide; ./Run.manu
diffing crn.mol2.save with crn.mol2
PASSED
==============================================================
cd disulfide; ./Run.auto.H
diffing crn.H.mol2.save with crn.H.mol2
PASSED
==============================================================
diffing crn.top.save with crn.top
PASSED
==============================================================
diffing crn.xyz.save with crn.xyz
PASSED
==============================================================
cd propdiol; ./Run.test1
diffing mol.prmtop.save with mol.prmtop
PASSED
==============================================================
diffing test1.out.save with test1.out
PASSED
==============================================================
cd propdiol; ./Run.test2
diffing mol2.prmtop.save with mol2.prmtop
PASSED
==============================================================
diffing test2.out.save with test2.out
PASSED
==============================================================
cd glycam; ./Run.test1
diffing n.pdb.save with n.pdb
PASSED
==============================================================
cd transform; ./Run.translate
diffing meoh_trans1.mol2.save with meoh_trans1.mol2
PASSED
==============================================================
diffing meoh_trans2.mol2.save with meoh_trans2.mol2
PASSED
==============================================================
cd 14scale; ./Run.14scale_test1
diffing nma1.prmtop.save with nma1.prmtop
PASSED
==============================================================
cd 14scale; ./Run.14scale_test2
diffing nma2.prmtop.save with nma2.prmtop
PASSED
==============================================================
./cpTESTF.sh
make[2]: Leaving directory `/usr/local/amber11/AmberTools/test/sleap'
cd resp && ./Run.ade
RESP stage 1:
diffing ade_1st.out.save with ade_1st.out
PASSED
==============================================================
diffing ade_1st.pch.save with ade_1st.pch
PASSED
==============================================================
diffing ade_1st_calc.esp.save with ade_1st_calc.esp
PASSED
==============================================================
RESP stage 2:
diffing ade_1st.chg.save with ade_1st.chg
PASSED
==============================================================
diffing ade_2nd.out.save with ade_2nd.out
PASSED
==============================================================
diffing ade_2nd.pch.save with ade_2nd.pch
PASSED
==============================================================
diffing ade_2nd.chg.save with ade_2nd.chg
PASSED
==============================================================
cd pbsa_dmp && ./Run.dmp.min
diffing mdout.dmp.min.save with mdout.dmp.min
PASSED
==============================================================
cd pbsa_lpb && ./Run.lsolver.min
bcoption=5 solvopt=1
diffing out.save/mdout.min_bc5_solv1.save with mdout.min_bc5_solv1
PASSED
==============================================================
bcoption=5 solvopt=2
diffing out.save/mdout.min_bc5_solv2.save with mdout.min_bc5_solv2
PASSED
==============================================================
bcoption=5 solvopt=3
diffing out.save/mdout.min_bc5_solv3.save with mdout.min_bc5_solv3
PASSED
==============================================================
bcoption=5 solvopt=4
diffing out.save/mdout.min_bc5_solv4.save with mdout.min_bc5_solv4
PASSED
==============================================================
bcoption=6 solvopt=1
diffing out.save/mdout.min_bc6_solv1.save with mdout.min_bc6_solv1
PASSED
==============================================================
bcoption=6 solvopt=3
diffing out.save/mdout.min_bc6_solv3.save with mdout.min_bc6_solv3
PASSED
==============================================================
bcoption=6 solvopt=4
diffing out.save/mdout.min_bc6_solv4.save with mdout.min_bc6_solv4
PASSED
==============================================================
cd pbsa_tsr && ./Run.tsrb.min
diffing mdout.tsrb.min.save with mdout.tsrb.min
PASSED
==============================================================
cd pbsa_radi && ./Run.ion.min
diffing ./out.save/Li.out.save with Li.out
PASSED
==============================================================
diffing ./out.save/Na.out.save with Na.out
PASSED
==============================================================
diffing ./out.save/K.out.save with K.out
PASSED
==============================================================
diffing ./out.save/Rb.out.save with Rb.out
PASSED
==============================================================
diffing ./out.save/Cs.out.save with Cs.out
PASSED
==============================================================
diffing ./out.save/F.out.save with F.out
PASSED
==============================================================
diffing ./out.save/Cl.out.save with Cl.out
PASSED
==============================================================
diffing ./out.save/IM.out.save with IM.out
PASSED
==============================================================
diffing ./out.save/Br.out.save with Br.out
PASSED
==============================================================
diffing ./out.save/I.out.save with I.out
PASSED
==============================================================
diffing ./out.save/MG.out.save with MG.out
PASSED
==============================================================
diffing ./out.save/Ca.out.save with Ca.out
PASSED
==============================================================
diffing ./out.save/Zn.out.save with Zn.out
PASSED
==============================================================
diffing ./out.save/tp3.out.save with tp3.out
PASSED
==============================================================
diffing ./out.save/ile.out.save with ile.out
PASSED
==============================================================
diffing ./out.save/leu.out.save with leu.out
PASSED
==============================================================
diffing ./out.save/val.out.save with val.out
PASSED
==============================================================
diffing ./out.save/phe.out.save with phe.out
PASSED
==============================================================
diffing ./out.save/trp.out.save with trp.out
PASSED
==============================================================
diffing ./out.save/hid.out.save with hid.out
PASSED
==============================================================
diffing ./out.save/hie.out.save with hie.out
PASSED
==============================================================
diffing ./out.save/nhe.out.save with nhe.out
PASSED
==============================================================
diffing ./out.save/tyr.out.save with tyr.out
PASSED
==============================================================
diffing ./out.save/ser.out.save with ser.out
PASSED
==============================================================
diffing ./out.save/thr.out.save with thr.out
PASSED
==============================================================
diffing ./out.save/cys.out.save with cys.out
PASSED
==============================================================
diffing ./out.save/cyx.out.save with cyx.out
PASSED
==============================================================
diffing ./out.save/met.out.save with met.out
PASSED
==============================================================
diffing ./out.save/lyn.out.save with lyn.out
PASSED
==============================================================
diffing ./out.save/ash.out.save with ash.out
PASSED
==============================================================
diffing ./out.save/glh.out.save with glh.out
PASSED
==============================================================
diffing ./out.save/asn.out.save with asn.out
PASSED
==============================================================
diffing ./out.save/gln.out.save with gln.out
PASSED
==============================================================
diffing ./out.save/nma.out.save with nma.out
PASSED
==============================================================
diffing ./out.save/alabk.out.save with alabk.out
PASSED
==============================================================
diffing ./out.save/glybk.out.save with glybk.out
PASSED
==============================================================
diffing ./out.save/probk.out.save with probk.out
PASSED
==============================================================
diffing ./out.save/da.out.save with da.out
PASSED
==============================================================
diffing ./out.save/dc.out.save with dc.out
PASSED
==============================================================
diffing ./out.save/dg.out.save with dg.out
PASSED
==============================================================
diffing ./out.save/dt.out.save with dt.out
PASSED
==============================================================
diffing ./out.save/ru.out.save with ru.out
PASSED
==============================================================
diffing ./out.save/arg.out.save with arg.out
PASSED
==============================================================
diffing ./out.save/asp.out.save with asp.out
PASSED
==============================================================
diffing ./out.save/cym.out.save with cym.out
PASSED
==============================================================
diffing ./out.save/glu.out.save with glu.out
PASSED
==============================================================
diffing ./out.save/hip.out.save with hip.out
PASSED
==============================================================
diffing ./out.save/lys.out.save with lys.out
PASSED
==============================================================
diffing ./out.save/dap.out.save with dap.out
PASSED
==============================================================
diffing ./out.save/da3p.out.save with da3p.out
PASSED
==============================================================
diffing ./out.save/da5p.out.save with da5p.out
PASSED
==============================================================
diffing ./out.save/danp.out.save with danp.out
PASSED
==============================================================
diffing ./out.save/rap.out.save with rap.out
PASSED
==============================================================
diffing ./out.save/ra3p.out.save with ra3p.out
PASSED
==============================================================
diffing ./out.save/ra5p.out.save with ra5p.out
PASSED
==============================================================
diffing ./out.save/ranp.out.save with ranp.out
PASSED
==============================================================
cd pbsa_npb && ./test
pbsa.ncg.bc5
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.ncg.bc6
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.nsor.bc5
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.nsor.bc6
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.asor.bc5
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.asor.bc6
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.dsor.bc5
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.dsor.bc6
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.ntmg.bc5
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.nticcg.bc5
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
pbsa.nticcg.bc6
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
cd pbsa_frc && ./test
dbf_0.argasp
checking argasp force
PASSED
dbf_0.dadt
checking dadt force
PASSED
dbf_0.dgdc
checking dgdc force
PASSED
dbf_0.lysasp
checking lysasp force
PASSED
dbf_0.polyALA
checking polyALA force
PASSED
dbf_0.polyAT
checking polyAT force
PASSED
dbf_1.argasp
checking argasp force
PASSED
dbf_1.dadt
checking dadt force
PASSED
dbf_1.dgdc
checking dgdc force
PASSED
dbf_1.lysasp
checking lysasp force
PASSED
dbf_1.polyALA
checking polyALA force
PASSED
dbf_1.polyAT
checking polyAT force
PASSED
dbf_2.argasp
checking argasp force
PASSED
dbf_2.dadt
checking dadt force
PASSED
dbf_2.dgdc
checking dgdc force
PASSED
dbf_2.lysasp
checking lysasp force
PASSED
dbf_2.polyALA
checking polyALA force
PASSED
dbf_2.polyAT
checking polyAT force
PASSED
cd pbsa_ipb2 && ./Run.110D.min
diffing mdout.110D.min.save with mdout.110D.min
PASSED
==============================================================
cd pbsa_delphi && ./Run.1az6.min
diffing mdout.1az6.min.save with mdout.1az6.min
PASSED
==============================================================
cd ambpdb && ./Run.ambpdb
| New format PARM file being parsed.
| Version = 1.000 Date = 02/19/04 Time = 15:33:29
diffing restrt.pdb.save with restrt.pdb
PASSED
==============================================================
cd ambpdb_first_protein && ./Run.ambpdb
| New format PARM file being parsed.
| Version = 1.000 Date = 02/15/07 Time = 16:57:28
diffing first.pdb.save with first.pdb
PASSED
==============================================================
cd ambpdb_first_rna && ./Run.ambpdb
| New format PARM file being parsed.
| Version = 1.000 Date = 05/18/06 Time = 18:52:52
diffing first.pdb.save with first.pdb
PASSED
==============================================================
cd elsize && ./Run.elsize
diffing elsize_out.trxox.save with elsize_out.trxox
PASSED
==============================================================
cd ./chamber/trans-but-2-ene && ./Run
/bin/rm: No match.
diffing chamber.out.save with chamber.out
PASSED
==============================================================
diffing prmtop.save with prmtop
PASSED
==============================================================
diffing inpcrd.save with inpcrd
PASSED
==============================================================
cd ./chamber/ala_ala_ala && ./Run
/bin/rm: No match.
diffing chamber.out.save with chamber.out
PASSED
==============================================================
diffing prmtop.save with prmtop
PASSED
==============================================================
diffing inpcrd.save with inpcrd
PASSED
==============================================================
cd ./chamber/poly_pro_gas && ./Run.poly_pro_gas_chamber
diffing chamber.crd.out.save with chamber.crd.out
PASSED
==============================================================
diffing poly_pro_gas_all22.crd.prmtop.save with poly_pro_gas_all22.crd.prmtop
PASSED
==============================================================
diffing poly_pro_gas_all22.crd.inpcrd.save with poly_pro_gas_all22.crd.inpcrd
PASSED
==============================================================
diffing chamber.pdb.out.save with chamber.pdb.out
PASSED
==============================================================
diffing poly_pro_gas_all22.pdb.prmtop.save with poly_pro_gas_all22.pdb.prmtop
PASSED
==============================================================
diffing poly_pro_gas_all22.pdb.inpcrd.save with poly_pro_gas_all22.pdb.inpcrd
PASSED
==============================================================
cd ./chamber/glucose && ./Run
/bin/rm: No match.
diffing chamber.out.save with chamber.out
PASSED
==============================================================
diffing prmtop.save with prmtop
PASSED
==============================================================
diffing inpcrd.save with inpcrd
PASSED
==============================================================
cd ./chamber/dhfr_gas && ./Run.dhfr_gas_chamber
diffing chamber.out.save with chamber.out
PASSED
==============================================================
diffing dhfr_gas_all22_prot.prmtop.save with dhfr_gas_all22_prot.prmtop
PASSED
==============================================================
diffing dhfr_gas_all22_prot.inpcrd.save with dhfr_gas_all22_prot.inpcrd
PASSED
==============================================================
cd ./chamber/dhfr_cmap_pbc && ./Run.dhfr_cmap_pbc_chamber
/bin/rm: No match.
diffing chamber.out.save with chamber.out
PASSED
==============================================================
diffing prmtop.save with prmtop
PASSED
==============================================================
diffing inpcrd.save with inpcrd
PASSED
==============================================================
cd ./sqm/c2h2 && ./Run
diffing c2h2.pm3.sp.out.save with c2h2.pm3.sp.out
PASSED
==============================================================
diffing c2h2.pm6.sp.out.save with c2h2.pm6.sp.out
PASSED
==============================================================
diffing c2h2.pm3.go.out.save with c2h2.pm3.go.out
PASSED
==============================================================
diffing c2h2.pm6.go.out.save with c2h2.pm6.go.out
PASSED
==============================================================
cd ./sqm/ch3f && ./Run
diffing ch3f.pm3.sp.out.save with ch3f.pm3.sp.out
PASSED
==============================================================
diffing ch3f.pm6.sp.out.save with ch3f.pm6.sp.out
PASSED
==============================================================
diffing ch3f.pm3.go.out.save with ch3f.pm3.go.out
PASSED
==============================================================
diffing ch3f.pm6.go.out.save with ch3f.pm6.go.out
PASSED
==============================================================
cd ./sqm/nma && ./Run
diffing nma.pm3.sp.out.save with nma.pm3.sp.out
PASSED
==============================================================
diffing nma.pm6.sp.out.save with nma.pm6.sp.out
PASSED
==============================================================
diffing nma.pm3.go.out.save with nma.pm3.go.out
PASSED
==============================================================
diffing nma.pm6.go.out.save with nma.pm6.go.out
PASSED
==============================================================
cd ./rism1d/spc && ./Run.spc
diffing spc.xvv.save with spc.xvv
PASSED
==============================================================
cd ./rism1d/spc && ./Run.spc-nacl
diffing spc-nacl.xvv.save with spc-nacl.xvv
PASSED
==============================================================
cd ./rism1d/tip3p && ./Run.tip3p
diffing tip3p.xvv.save with tip3p.xvv
PASSED
==============================================================
cd ./rism1d/tip3p && ./Run.tip3p-nacl
diffing tip3p-nacl.xvv.save with tip3p-nacl.xvv
PASSED
==============================================================
Finished test suite for AmberTools at Mon Mar 7 16:11:27 CET 2011.
make[1]: Target `test.serial' not remade because of errors.
make[1]: Leaving directory `/usr/local/amber11/AmberTools/test'
276 file comparisons passed
4 file comparisons failed
64 tests experienced errors
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Received on Mon Mar 07 2011 - 11:00:02 PST
