And then you could filter out the cases with bad steric clashes by
rejecting anything that won't minimize.
Bill
Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> I suppose you could write a script that makes leap input with random values
> for the impose command. Do you really want random though? Many are quite
> bad.
> On Dec 14, 2012 2:22 PM, "Shashidhar Rao" <shashidharr.gmail.com> wrote:
>
> > I would like to know if it is possible to build a random conformation of a
> > peptide in AMBER (tleap) instead of the extended linear chain which can be
> > minimized and subjected to dynamics to generate arbitrary conformations.
> >
> > thanks,
> > Shashi Rao
> >
> > --
> > Shashidhar N. Rao
> > 3 SERINA DRIVE
> > PLAINSBORO
> > NEW JERSEY 08536 USA
> >
> > shashidharr.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Dec 15 2012 - 11:00:02 PST
