Re: [AMBER] PCA analysis and amber prmtop file

From: Jason Swails <>
Date: Tue, 22 Oct 2013 07:58:07 -0400

On Tue, Oct 22, 2013 at 4:29 AM, Neha Gandhi <> wrote:

> Dear mailing list,
> I have a multiple pdb file with just the backbone atoms. I want to
> perform PCA analyses. For using PCA, ptraj will require .prmtop file.
> When I prepare .prmtop file it will write sidechains and backbone too.
> Is there a way to save only backbone atoms in .pmrtop file?

cpptraj allows you to use PDBs instead of topology files. In general,
there is no way to save only backbone atoms in a prmtop file, but you can
typically specify masks (that select only the backbone atoms, for
instance), when performing these types of analyses with either ptraj or


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Oct 22 2013 - 05:00:04 PDT
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