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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 17 2015 - 09:30:03 PDT
