On Sun, Oct 2, 2011 at 1:18 PM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Sep 30, 2011, Jason Swails wrote:
>
> > The program I wrote, parmed.py, should be easy to use (hopefully) because
> it
> > operates just like ptraj and cpptraj (only instead of playing with
> > trajectories it plays with topology files).
>
> Sounds great! Can you ask it to strip certain residues, then output the
> corresponding prmtop? Of can ptraj/cpptraj now do this? [I need a "real"
> prmtop, not just for visualization.]
>
I've been dragging my feet to add that functionality because it requires
altering a lot (every?) section of the topology file, which I would then
have to generalize to chamber prmtops as well. I plan to start with
stripping solvent and ions and then to extend it to individual molecules in
the solute (such as stripping a non-covalently bound ligand out of a complex
topology file for MM/PBSA-like purposes), but I don't know how you could
generalize removing an internal residue and then cap it (or do you not have
to cap it? that doesn't seem very physical to me...). This should
(hopefully) all be in before the code freeze.
All the best,
Jason
> ...thanks....dac
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Oct 02 2011 - 13:30:03 PDT
