Hi,
As of AmberTools 12 cpptraj will write out a fully functional stripped
topology file. Any interactions involving stripped atoms are also
removed, although the parameters are still there (they are just not
accessed).
Note that parmed.py also allows you to strip topologies.
-Dan
On Tue, Mar 26, 2013 at 8:25 AM, Ignacio J. General <ijgeneral.gmail.com> wrote:
> Dear Amber users:
>
> I remember that sometime ago cpptraj was able to strip atoms from the
> prmtop file, but it was suggested that we use that only for visualization
> purposes, not for simulations. Is this still the case? Or I can use a
> stripped prmtop for simulations?
>
> And in case I can use it for MD, when I strip some residue in a protein, do
> I need to first remove the bonds connecting that residue to the others, or
> is this done automatically by cpptraj?
>
> Thanks,
>
> Ignacio
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--
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Tue Mar 26 2013 - 08:00:03 PDT
