Hi,
Cpptraj doesn't currently handle the '.xtc' format (on the ToDo list)
but it will read PDB files just fine. You could concatenate your PDB
files using cpptraj into a format that mmpbsa.py will understand, like
NetCDF, e.g.:
parm frame1.pdb
trajin frame1.pdb
trajin frame2.pdb
...
trajin frameX.pdb
trajout AllFrames.nc
Hope this helps,
-Dan
On Mon, Mar 21, 2016 at 11:01 PM, Suchetana Gupta <tutulg.gmail.com> wrote:
> Dear AMBER Users
> I have a set of simulations performed using Gromacs. My trajectory is in
> the .xtc format and topology is in .tpr format. The entire trajectory is
> also present in PDB format. I want to calculate pairwise interaction energy
> using MMPBSA. How can I go about it?
> (I have used g_mmpbsa in Gromacs; however, pairwise decomposition is not
> possible to give a n*n matrix of energy values)
> Thanks in advance for the help.
> Regards
> Suchetana Gupta
> PhD Scholar
> IIT Madras
> _______________________________________________
> 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 307
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 Tue Mar 22 2016 - 08:00:03 PDT
