Hi,
I think MMPBSA.py should be able to handle DCD files since it uses
cpptraj as a back-end for trajectory processing, and cpptraj handles
DCD/PSF files just fine (MMPBSA experts correct me if I'm wrong). You
should be able to convert your PSF to an Amber topology with the
'chamber' program.
-Dan
On Fri, Sep 13, 2013 at 8:45 AM, sudipta <sudipta.mml.gmail.com> wrote:
> Hi All,
>
> I want to use MMPBSA.py script for calculating the free energy of binding
> between protein and ligand. However, I generated the trajectory of my
> system using NAMD program and CHARMM force field. Therefore, I have only
> .psf, .dcd and charmm parammeter files. Is there any way to use MMPBSA.py
> program for this trajectory.
>
> Moreover, are there any ambertools that convert .psf to .prmtop file?
>
> thanks in advance
> Sudipta
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--
-------------------------
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) 585-9119 (Fax)
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Received on Fri Sep 13 2013 - 08:30:03 PDT
