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

From: Wesley Michael Botello-Smith <>
Date: Fri, 20 Jul 2018 16:56:51 -0700

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 <> 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
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Received on Fri Jul 20 2018 - 17:00:02 PDT
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