[AMBER] MMPBSA.py QM entropy calculation error

From: Nic Steussy <csteussy.purdue.edu>
Date: Thu, 5 Nov 2015 14:35:28 -0500

   I am experimenting with using entropy=1 with MMPBSA.py to calculate the
   entropy term in the binding energy of a ligand to a protein. However, every
   time I run the program it uses an enormous amount of memory (15GB on my 16GB
   workstation) and then crashes with std::bad_alloc.
   This appears to be a C memory error. I am uncertain if it is a memory leak
   or that perhaps my system is too large to use QM.
   I am using Ambertools 15, completely patched.
   My system is a 46kda protein in a hydrated dimer complex binding a small
   molecule (monomer 6307 atoms, dimer + waters ~82760 atoms).
   Suggestions welcomed.
   Nic out
      keep_files=2, endframe=15, entropy=1,
     igb=2, saltcon=0.100,
     istrng=0.100, inp=1, radiopt=0,
   mpirun -np 4 --bind-to-none $AMBERHOME/bin/MMPBSA.py.MPI -O -i qha.in\
    -o qha_15frames.dat\
    -sp ../complex-wat.top \
    -srp ../protein-wat.top \
    -slp ../ligand-wat.top \
    -cp ../complex.top \
    -rp ../protein.top \
    -lp ../ligand.top \
    -y ../complex_prodc.mdcrd.gz \
    -yr ../protein_prodc.mdcrd.gz \
    -yl ../ligand_prodc.mdcrd.gz
C. Nicklaus Steussy, M.D., Ph.D.
Purdue University
   1. mailto:csteussy.purdue.edu
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Received on Thu Nov 05 2015 - 12:00:04 PST
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