Thanks Daniel. Just one more question. How is it that the stripped bond
parameters are still there but not used? Is there some kind of flag telling
pmemd (or sander) not to use them?
Ignacio
On Tue, Mar 26, 2013 at 10:34 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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
> (801) 585-9119 (Fax)
>
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Received on Tue Mar 26 2013 - 08:00:04 PDT
