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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Received on Fri May 08 2015 - 04:00:03 PDT
