Re: [AMBER] Monitoring pi-cationic interaction

From: Daniel Roe <>
Date: Sun, 30 Nov 2014 12:01:11 -0700


One potential way would be to use the 'hbond' command. You could use
the 'donormask', 'donorhmask', and 'acceptormask' keywords to define
ring atoms, then use the 'solventdonor' and 'solventacceptor' keywords
to define the ions, and specify 'nointramol' to ignore intramolecular
interactions. For example, say you wanted to monitor potential Na+ to
PHE interactions:

hbond donormask :PHE.%CA donorhmask :PHE.%HA acceptormask :PHE.%CA \
  solventdonor :Na+ solventacceptor :Na+ nointramol \
  out nhbvtime.dat avgout hbavg.dat

FYI the '.%' mask construct selects atoms by type.

The only downside to this is you will get multiple results for the
same interaction since several atoms on an aromatic ring may have
distances to the same ion at one time that satisfy the cutoff, so
you'll have to be careful with how you parse your results.


PS - Of course, keep in mind that in a pairwise-additive MM force
field there are no "real" cation-pi interactions, since all
electrostatics are simple point charge interactions.

On Sat, Nov 29, 2014 at 12:12 AM, asdda asa <> wrote:
> Dear Amber user;
> Please anyone know how to monitor pi-cationic interactions during md using
> ptraj.
> Any help would be highly appreciated.
> best!
> nadaafiva
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Nov 30 2014 - 11:30:02 PST
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