Hi,
How many frames are in the original trajectory itself? You can easily find
out in cpptraj via:
cpptraj <topology file>
> trajin <trajectory>
[<trajectory>] contains X frames.
Also, what patches have been applied (output of $AMBERHOME/update_amber
--version)?
-Dan
On Sat, Mar 15, 2014 at 8:34 PM, manikanthan bhavaraju <mhb75.msstate.edu>wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Mar 15 2014 - 21:30:02 PDT
