Hi,
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,
-Dan
On Fri, Jul 13, 2018 at 6:14 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
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Received on Fri Jul 20 2018 - 08:30:02 PDT
