$AMBERHOME/update_amber --version gave the following
Version is reported as <version>.<patches applied>
AmberTools version 13.23
I trajectory contains only 400 frames. I found using cpptraj. Now it makes
sense. Thanks for the help.
mani
On Sun, Mar 16, 2014 at 12:08 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Sat Mar 15 2014 - 22:00:02 PDT
