Hi Daniel,
Yes, you are right. I can able to convert DCD file to amber .mdcrd file.
But I can't convert the .prmtop file from .psf and charm parameter files.
As far as I know there is some limitation on MMPBSA program which uses only
amber .prmtop file. If you have any idea how to do that please let me know.
Thanks again
Sudipta
On Fri, Sep 13, 2013 at 11:14 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > 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) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 13 2013 - 08:30:03 PDT
