Hi Takeshi,
I could not see the attachment. Which program did you use? Is it MCPB or
MCPB.py?
Best,
Pengfei
2015-05-08 6:33 GMT-04:00 Takeshi Baba <tbaba.cheng.es.osaka-u.ac.jp>:
> Dear amber users,
>
> I try to obtain the resp charge by using MCPB program.
> However the program does not work normally.
> Moreover, the error comment is only "Segmentation fault"
>
> I could not solve this problem
>
> I attach my using files.
>
>
> Do you have any advices for me?
>
> Best regards
> Takeshi Baba
>
> --------------------------------------------------------------------------------------------------------
> Takeshi Baba, Ph. D.
> Division of Chemical Engineering,
> Department of Materials Engineering Science,
> Graduate School of Engineering Science,
> Osaka University, Toyonaka, Osaka 560-8531, JAPAN
> Tel: +81-6-6850-6266, Fax: +81-6-6850-6268
> E-mail: tbaba.cheng.es.osaka-u.ac.jp
>
> --------------------------------------------------------------------------------------------------------
>
>
>
>
> 2015/05/08 2:02、Ramin Ekhteiari <ramin_ekh.yahoo.com> のメール：
>
> > 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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> >
> >
> >
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--
Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
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Received on Fri May 08 2015 - 08:00:03 PDT
