Re: [AMBER] RAM error during multiple MMGBSA runs

From: Ray Luo, Ph.D. <ray.luo.uci.edu> Date: Thu, 2 Oct 2014 13:24:05 -0700

--
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
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