Thanks so much, Prof.
I will try it.
Best!
nadaafiva
On Mon, Dec 1, 2014 at 3:01 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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.
>
> -Dan
>
> 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 <nadaafiva.gmail.com> 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> 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 Sun Nov 30 2014 - 20:00:02 PST
