[AMBER] RAM error during multiple MMGBSA runs

From: James Starlight <jmsstarlight.gmail.com>
Date: Thu, 2 Oct 2014 09:36:05 +0200

Dear Amber users!

I've faced with some problem assosiated with the RAM error during MM-GBSA

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
  # 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}

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?

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