Dear Jason,
I greatly appreciate your taking time.
I interestingly solved the problem using following way
I cleaned Ambertools15, and instead I tried to install Ambertools14 and then updated it. Now it works well.
Thanks
On Thursday, May 7, 2015 4:12 PM, Jason Swails <jason.swails.gmail.com> wrote:
OK, I think I fixed the main problem, but for some reason none of the
MMPBSA.py tests pass for me with Python 2.4 and I can't figure out what
the problem is.
Can you try the proposed update and see if it fixes MMPBSA.py for you?
To do this, go to $AMBERHOME and run the command:
./update_amber --apply
http://ambermd.org/test_updates/update.1
Then make sure to recompile AmberTools 15 before trying to run your
test.
Thanks,
Jason
On Thu, 2015-05-07 at 06:32 +0000, Ramin Ekhteiari wrote:
> Hi
>
> Below is the contents of AMBERHOME/bin
> acdoctor cpptraj.log make_crd_hg MMPBSA.py.MPI OptC4.py resp sviol2addles cpptraj.MPI makeDIP_RST.cyana mmpbsa_py_nabnmode paramfit respgen teLeap
> add_pdb database makeDIST_RST mm_pbsa_statistics.pl parmcal rism1d test.py
> AddToBox elsize matextract molsurf parmchk rism3d.snglpnt tinker_to_amber
> am1bcc espgen matgen mpinab parmchk2 sander tleap
> amber.csh exceptions.py matmerge mpinab2c parmed.py sander.LES transform
> amber.sh exceptions.pyc matmul MTKppConstants pbsa sander.LES.MPI translate
> ambmask fantasian MCPB nab pdb4amber sander.MPI tss_init
> ambpdb FEW.pl MCPB.py nab2c pdbSearcher saxs tss_main
> antechamber ffgbsa mdgx nc-config PdbSearcher.py saxs_md tss_next
> ante-MMPBSA.py fftw-wisdom mdgx.MPI nccopy prep2xml senergy ucpp
> atomtype fftw-wisdom-to-conf mdnab ncdump prepgen sequenceAligner UnitCell
> bondtype fix_new_inpcrd_vel mdout2pymbar.pl ncgen process_mdout.perl sgldinfo.sh xaLeap
> capActiveSite frcmod2xml mdout_analyzer.py ncgen3 process_minout.perl sgldwt.sh xleap
> charmmgen func minab nef_to_RST PropPDB softcore_setup.py xparmed.py
> charmmlipid2amber.py gbnsr6 mmE new2oldparm protonator sqm yacc
> ChBox hcp_getpdb mm_pbsa_nabnmode new_crd_to_dyn pymdpbsa stats
> cphstats hybrid mm_pbsa.pl new_to_old_crd pytleap stdLib2Sdf
> cpinutil.py makeANG_RST MMPBSA.py nf-config reduce superimposer
> cpptraj makeCHIR_RST mmpbsa_py_energy nmode residuegen sviol
>
> ls $AMBERHOME/lib/python*/site-packages/
> argparse.py chemistry compat24.pyc fortranformat mcpb MMPBSA_mods ParmedTools pymsmtexp.pyc pymsmtmol sanderles
> argparse.pyc compat24.py cpinutils interface mdoutanalyzer mpi4py pymsmtexp.py pymsmtlib sander
>
> Version of Python
> Python 2.4.3
> ThanksBerk
>
>
>
>
> On Thursday, May 7, 2015 4:47 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> On Wed, May 6, 2015 at 5:06 PM, Ramin Ekhteiari <ramin_ekh.yahoo.com> wrote:
>
> > I have addressed "the path of AMBERHOME" by export
> > AMBERHOME=/RS/users/myurtsever/stbknm/amber12/amber15tools/amber14
> > and have sourced the amber.sh (source
> > /RS/users/myurtsever/stbknm/amber12/amber15tools/amber14/amber.sh)
> > But the same problem has been appeared.
> >
>
> What are the contents of $AMBERHOME/bin? (Type "ls $AMBERHOME/bin" and
> print the contents here).
>
> Also, what are the results of the following commands:
>
> python --version
> echo $PYTHONPATH
> ls $AMBERHOME/lib/python*/site-packages/
> python -m MMPBSA_mods
>
>
>
> >
> > Interestingly on this system I use ambertools 13 and it works well, but I
> > do not know why the new version (15) does not.
> >
>
> The location where Python modules are stored was changed from
> $AMBERHOME/bin to $AMBERHOME/lib/pythonX.X/site-packages, and the amber.sh
> file appropriately updates your environment for this change.
>
> HTH,
> Jason
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 07 2015 - 10:30:03 PDT
