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
Received on Thu Oct 02 2014 - 01:00:02 PDT
