Dear All,
I am trying to calculate the binding free energy of a ligand bound to a
membrane protein using mmpbsa.py script of Ambertools13. By using the last
10 ns of the equilibration, I would like to generate 500 snapshots for
GBSA calculations. The following is the mmpbsa.py input file:
GB
&general
endframe=500, verbose=1,
/
&gb
igb=5, saltcon=0.100,
/
However, cpptraj is only generation 400 frames as shown below:
Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
400 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/srg/mhb75/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
And so on....
Hence, I tired to debug the problem and performed GBSA calcutions using
100, 200, 300, and 400 frames. All the calculations ran successfully.
However, when I tired to calculate binding free energy using 500 frames.
Again I am getting the result as shown above. I am not sure why cpptraj is
unable to generate 500 frames ?? Please let me know if anybody knows how
to fix it.
Thanks,
mani
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Received on Sat Mar 15 2014 - 20:00:02 PDT
