Re: [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers

From: Daniel Roe <>
Date: Fri, 20 Jul 2018 11:03:41 -0400


The 'nativecontacts' command may help. It doesn't take things like
charge into account (this is a potentially interesting future
functionality upgrade), it just uses simple distance cutoffs, but it
could be a good first pass. You may also be able to adapt the 'hbond'
command but without knowing the specifics of the system I can't
provide specific details.

Hope this helps,


On Fri, Jul 13, 2018 at 6:14 PM, Sally Pias <> 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 mailing list
Received on Fri Jul 20 2018 - 08:30:02 PDT
Custom Search