I'm not sure if there's a ready-made or almost-there way in AMBER.
Maybe someone else can speak to that. I suppose you saw that ptraj
will calculate the dipoles for you. You can do it pretty easily using
GLYLIB if you know a little C and have a prmtop and trajectory saved.
It would be a little more work with a bunch of pdb's, but not awful.
If MMTK (Python) would also be a quick fix, someone else will have to
speak up.
There are already glylib functions to read amber prmtop files, load in
coordinates, calculate point charge dipoles and do some vector math
(like dot products). You might have to write a little code, but
probably not much, mostly loops and simple math. Write me offline if
you want to use it and have questions. (
http://glycam.org/glylib)
On the other hand, if someone has ready-made, definitely do that.
:-) Lachele
On Tue, May 4, 2010 at 11:46 AM, Ganesh Kamath <gkamath9173.gmail.com> wrote:
> Hi all,
>
> Is there a way in amber to calculate the kirkwood G factor. This is
> basically a dot product of dipole moments
> of water. I would like to calculate this.
> If anyone could help me in this it would be grateful.
>
> thanks,
>
> ganesh
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue May 04 2010 - 11:00:05 PDT
