[AMBER] MMPBSA binding calculations

From: shenna shearin <smsheari.gmail.com>
Date: Wed, 9 Jun 2010 13:44:34 -0700

Greetings Amber community:

I am calculating the binding free energy of a protein-protein complex in
parallel. I was able to calculate the binding energy of the WT complex with
no problem but when I tried a mutated complex I encounter problems. I
created my gas phase and solvated topology and coordinate files as directed.
When I ran the script: mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i
mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp
ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd > progress.log 2>&1

using my own input files the calculation runs smoothly for a while cease. In
the output file 'progress.log' I see an error that states: The files have
been retained for debugging purposes. Type MMPBSA --clean to erase the
files. I need clarity on why this is happening and how to retify this
problem. Can someone please help. Thanks in advance.

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Received on Wed Jun 09 2010 - 14:00:03 PDT
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