On Mon, Jun 3, 2013 at 8:38 AM, Paul Driscoll <pdrisco.nimr.mrc.ac.uk>wrote:
> Hi,
>
> I plan to strip down my trajectory files to protein backbone amide NH
> atoms only. How do I prepare a prmtop for use in subsequent ptraj
> analysis? [In other words how do I prepare a prmtop for only a subset of
> protein atoms?]
>
As Marc suggested, parmstrip will do the trick (ParmEd also has a stripping
ability, but if you're already stripping a mask with cpptraj you might as
well use cpptraj to strip the topology, too).
I think it's even easier than that, though. In cpptraj, do your
stripping like this:
parm my.parm7
trajin mytraj.nc
strip !:N outprefix backbone_amide
trajout backbone_amide.nc
This will create a trajectory file 'backbone_amide.nc' and a matching
topology file backbone_amide.my.parm7.
However, I would be wary of stripping the coordinates down to _just_ a
single atom in each residue, since some actions in cpptraj make use of bond
information. If it was me, I would just strip out the solvent and leave
the entire solute intact and do any analyses you have using a specific atom
mask.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 03 2013 - 06:30:02 PDT
