Re: [AMBER] How do I use for namd .dcd file?

From: Daniel Roe <>
Date: Fri, 13 Sep 2013 09:14:37 -0600


I think 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.


On Fri, Sep 13, 2013 at 8:45 AM, sudipta <> wrote:
> Hi All,
> I want to use 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
> program for this trajectory.
> Moreover, are there any ambertools that convert .psf to .prmtop file?
> thanks in advance
> Sudipta
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Sep 13 2013 - 08:30:03 PDT
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