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

From: Sally Pias <sallypias.gmail.com>
Date: Tue, 24 Jul 2018 11:16:58 -0600

 Hi Dan, Wesley, and Hai -

Thank you all for your suggestions. The hbond command detected
charge-dipole interactions between phosphate O acceptors and O-H or N-H
donors. Nativecontacts also helped find headgroup phosphate-choline
interactions
-- achieved by setting mask1 and mask2 to the phosphate P and the choline
N. One other functionality that would be useful to me would be to record
the distance between atoms in the interactions detected. I want to know the
average headgroup-headgroup and headgroup-organic molecule interaction
distance in different bilayers.

Best,
Sally

--
Sally Pias
Assistant Professor of Chemistry
Faculty Adjunct, Department of Biology
New Mexico Tech
(575) 835-6204
www.nmt.edu/~spias
spias.nmt.edu
On Fri, Jul 20, 2018 at 6:01 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
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Received on Tue Jul 24 2018 - 10:30:02 PDT