Hi.....,!!!!????
Marcelo A. Chagas
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2015-08-17 13:05 GMT-03:00 Marcelo Andrade Chagas <andrade.mchagas.gmail.com
>:
> Dear Dan ...
>
> I had already installed the amber14 ...
>
> then I tried to update the latest version of ambertools15
>
> I used the command ./update_amber --upgrade "
>
> I noticed that the executable file MCPB.py was not created in the folder
> bin
>
> So I decided to reinstall the program by downloading the new amber
> AmberTools15
>
> then show the folders contained in the used directory.
>
> then follow the commands I used:
>
> [lqcmm.gibbs AMBER]$ ls
> amber14 Amber14.tar.bz2 AmberTools14.tar.bz2 AmberTools15.tar.bz2
>
>
> tar xvfj AmberTools15.tar.bz2
>
> tar xvfj Amber14.tar.bz2
>
> export AMBERHOME=/home/lqcmm/AMBER/amber14
>
> as I am using centOS (yum)
>
> sudo yum install csh flex gfortran g++ xorg-dev \
> zlib1g-dev libbz2-dev patch python-tk python-matplotlib
>
> after it appeared a message that no file was found
> to update as soon proceeded with the installation
>
> ./configure --help
>
> ./configure gnu
>
> source /home/lqcmm/AMBER/amber14/amber.sh
>
> make install
>
> make test
>
>
> It was informed that the installation was completed
>
> now appears in the bin folder executable MCPB.py
>
> [lqcmm.gibbs bin]$ ls
> acdoctor charmmgen fftw-wisdom
> makeDIST_RST mmE nccopy parmcal
> process_mdout.perl sander superimposer UnitCell
> addles charmmlipid2amber.py fftw-wisdom-to-conf
> matextract mm_pbsa_nabnmode ncdump parmchk
> process_minout.perl sander.LES sviol xaLeap
> add_pdb ChBox fix_new_inpcrd_vel
> matgen mm_pbsa.pl ncgen parmchk2
> PropPDB saxs sviol2 xleap
> AddToBox cphstats frcmod2xml
> matmerge MMPBSA.py ncgen3 parmed.py
> protonator saxs_md teLeap xparmed.py
> am1bcc cpinutil.py func
> matmul mmpbsa_py_energy nef_to_RST pbsa
> pymdpbsa senergy tinker_to_amber yacc
> ambmask cpptraj gbnsr6
> MCPB mmpbsa_py_nabnmode new2oldparm pdb4amber
> pytleap sequenceAligner tleap
> ambpdb database hcp_getpdb
> MCPB.py mm_pbsa_statistics.pl new_crd_to_dyn pdbSearcher
> reduce sgldinfo.sh transform
> antechamber elsize hybrid
> mdgx molsurf new_to_old_crd PdbSearcher.py
> residuegen sgldwt.sh translate
> ante-MMPBSA.py espgen makeANG_RST
> mdnab MTKppConstants nf-config pmemd
> resp softcore_setup.py tss_init
> atomtype fantasian makeCHIR_RST mdout2pymbar.pl
> nab nmode pmemd.amoeba respgen
> sqm tss_main
> bondtype FEW.pl make_crd_hg
> mdout_analyzer.py nab2c OptC4.py prep2xml
> rism1d stats tss_next
> capActiveSite ffgbsa makeDIP_RST.cyana
> minab nc-config paramfit prepgen
> rism3d.snglpnt stdLib2Sdf ucpp
> [lqcmm.gibbs bin]$
>
>
>
> however, when used MCPB.py program the following message appears:
>
> [lqcmm.gibbs bin]$ MCPB.py
>
> Traceback (most recent call last):
> File "/home/lqcmm/AMBER/amber14/bin/MCPB.py", line 46, in <module>
> from mcpb.gene_model_files import get_ms_resnames, gene_model_files
> ImportError: No module named mcpb.gene_model_files
>
>
>
>
> I hope to have clearer acid (desulpe by the English because I'm getting
> better)
>
> I await suggestions
>
> thanks
>
> Marcelo A. Chagas
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2015-08-17 12:24 GMT-03:00 Daniel Roe <daniel.r.roe.gmail.com>:
>
>> On Thu, Aug 13, 2015 at 1:14 PM, Marcelo Andrade Chagas
>> <andrade.mchagas.gmail.com> wrote:
>> > the updated version of Ambertools14 for 15 lowering of the site and the
>> > Ambertools15
>> > Amber reinstalling the program because the "./update_amber --upgrade"
>> has
>> > not worked.
>>
>> Just to be clear, do you mean you started a fresh installation of
>> AmberTools15 because the AmberTools14 -> 15 upgrade failed?
>>
>> > What could have been done wrong in install mode?
>>
>> Could you list what you did step-by-step (including the flags you
>> passed to configure etc). We may be able to better assist you if we
>> have more information.
>>
>> -Dan
>>
>> >
>> > Best regards
>> >
>> > Marcelo A.Chagas
>> >
>> > Marcelo Andrade Chagas, MSc
>> > (PhD student)
>> > Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
>> > * http://lqcmm.qui.ufmg.br/
>> > Departamento de Química da Universidade Federal de Minas Gerais - UFMG
>> > Tel:(31)3409-5776
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Aug 21 2015 - 08:30:06 PDT
