On Tue, Oct 22, 2013 at 4:29 AM, Neha Gandhi <n.gandhiau.gmail.com> 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
cpptraj.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 22 2013 - 05:00:04 PDT
