Just for clarity: pytraj works because it is cpptraj under the hood.
Hai
On Fri, Jul 20, 2018 at 7:57 PM Wesley Michael Botello-Smith <
wmsmith.uci.edu> wrote:
> nativecontacts works... pytraj can do this as well. If you want to ensure
> it is for ion to ion or ion to dipole, you can accomplish this using
> appropriate selection masks. I think, if you use the convert the contact
> map into a matrix, you can use that to compute aggregate cluster sizes.
>
> On Fri, Jul 13, 2018, 3:19 PM Sally Pias <sallypias.gmail.com> wrote:
>
> > Hi all,
> >
> > I am looking for a way to count contacts between phospholipid headgroups
> > and organic-lipid conjugate molecules embedded in a bilayer. Is there a
> > script or command similar to hbond that can calculate charge-charge and
> > ion-dipole contacts between nonsolvent residues (i.e., not water or
> > monatomic ions)? Aggregate contact counts, as well as number of contacts
> > over time would both be useful. Ideally, we need to be able to identify
> the
> > residues and atoms involved.
> >
> > Thanks,
> > Sally
> >
> > --
> > Sally Pias
> > Associate Professor of Chemistry
> > Faculty Adjunct, Department of Biology
> > New Mexico Tech
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 20 2018 - 17:30:01 PDT
