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

From: Jason Swails <>
Date: Fri, 13 Sep 2013 11:53:55 -0400

On Fri, Sep 13, 2013 at 11:28 AM, sudipta <> wrote:

> Hi Daniel,
> Yes, you are right. I can able to convert DCD file to amber .mdcrd file.

As Dan said, you do _not_ need to convert DCD files to amber .mdcrd since uses cpptraj for trajectory processing, so any trajectory
recognized by cpptraj is recognized by (this includes DCD).

> 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.

Yes, calls amber programs to compute energies, so you must use
Amber topology files. If you are using the CHARMM force field, then you
need to use chamber (see chapter 2, section 11 of the AmberTools 13 manual
near page 45 or so).

As a note, you will need to have Amber12 installed (with sander) in order
to use on a chamber-generated topology. The reason is that
CHARMM energy terms are only supported in sander and pmemd (not NAB, which
is the program in AmberTools that would otherwise use to compute


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Sep 13 2013 - 09:00:04 PDT
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