The previous issue have been solved ( the error was due incorect atoms
within amber mask's)
My next problem is on the ussage of the MMPBSA.py.MPI from the
amber-tools-12 built on open SUSE:
Here calling the program I've obtained:
gleb.gpu2:~/Documents/script/Analysis> MMPBSA.py.MPI
Fatal Error: I could not find the Python MPI package (mpi4py)! This means
that
it could not be built during the standard AmberTools
installation.
Check $AMBERHOME/src/AmberTools/mpi4py_install.log for errors.
I've tried to import mpi4py from the AMBERHOME or install it via package
manager but didn't find this module in both cases. Could you suggest me
most trivial solution?
James
2014-10-02 22:24 GMT+02:00 Ray Luo, Ph.D. <ray.luo.uci.edu>:
> Can you reproduce this error on a different server, maybe with a larger
> RAM?
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Thu, Oct 2, 2014 at 12:36 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > Dear Amber users!
> >
> >
> > I've faced with some problem assosiated with the RAM error during MM-GBSA
> > calculations
> >
> > Briefly my script performs in loop several MMPBSA calculations for
> several
> > systems and put some data from each result.log to some shared txt file
> >
> > In details you can find my script below
> >
> > #perform MMGBSA
> > for sim in ${analysis}/* ; do
> > simulation=$(basename "$sim")
> > pushd ${sim}
> > mkdir ${sim}/mmgbsa_${simulation}
> > cd ./mmgbsa_${simulation}
> > printf "&general\nstartframe= 1, interval=5, keep_files=2, entropy=1,
> > ligand_mask=:MOL, receptor_mask=:1-289, strip_mask=:WAT:Cl-:NA+:K+:PPC,
> > netcdf=1\n/\n&gb\nigb=2, saltcon=0.100,\n/\n" > ./mmgbsa.in
> > echo "MMPBSA of ${simulation} is in a progress!"
> > ante-MMPBSA.py -p ../protein.parm7 -c ../protein.inpcrd -c
> complex.prmtop
> > -r receptor.prmtop -l ligand.prmtop -s :WAT:Cl-:NA+:K+:PPC -n :MOL
> > MMPBSA.py -O -i mmgbsa.in -o mmgbsa_${simulation}.dat -sp
> > ../protein.parm7 -cp complex.prmtop -rp receptor.prmtop -y ../md.nc -lp
> > ligand.prmtop
> > # remove something unussed files but not the log with the free
> energies!!
> > rm -f ./_MMPBSA_*
> > echo "For ${simulation}" >> ${analysis}/final_mmgbsa.txt
> > cat mmgbsa_${simulation}.dat |tail -n 3 >>
> ${analysis}/final_mmgbsa.txt
> > cd ..
> > mv ${analysis}/${sim}/mmgbsa_${simulation}
> > ${analysis}/mmgbsa_${simulation}
> > popd
> > done
> >
> >
> >
> > eventually after several such calculations I've received:
> >
> >
> > *** Error in `/+SOFTWARE/amber12/bin/mmpbsa_py_energy': malloc(): memory
> > corruption: 0x0000000001546800 ***
> >
> > Are there any possibilities to free RAM each time after previous
> > calculation have been finished?
> >
> > James
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 03 2014 - 02:00:02 PDT
