All,
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
==============
&general
keep_files=2, endframe=15, entropy=1,
/
&gb
igb=2, saltcon=0.100,
/
&pb
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]csteussy.purdue.edu
================================
References
1. mailto:csteussy.purdue.edu
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Received on Thu Nov 05 2015 - 12:00:04 PST
