> One other functionality that would be useful to me would be to record
> the distance between atoms in the interactions detected.
I used pytraj to do something essentially like this.
When you use native contacts in pytraj it will spit out either an
OrderedDictionary or pandas.DataFrame object for you.
>From that you can build up a set of 'distance' or 'vector' commands that
you can feed to pytraj.compute or pytraj.pmap.
Again, this would yield a corresponding OrderedDictionary or DataFrame
object that you can analyze appropriately.
Alternatively, you could load your output csv or data table generated by
the cpptraj HBond or nativecontacts command into python using
'pandas.read_csv' and start from there if you don't want to re-run the
native-contacts command in pytraj.
-Wes
On Tue, Jul 24, 2018 at 10:16 AM, Sally Pias <sallypias.gmail.com> wrote:
> 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
> > > > _______________________________________________
> > > > 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
> >
> _______________________________________________
> 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 Tue Jul 24 2018 - 11:00:02 PDT
