Thanks David,
Your reply helped a lot.
On Tue, Dec 31, 2013 at 12:28 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Dec 31, 2013, Sourav Purohit wrote:
>
> > Is it possible to define angle restraints using atom groups.
>
> I believe this is possible in sander but not pmemd.
>
> > If I choose to define angle restraint using three atoms, then how is the
> > angle defined?? Is it the angle between the vectors corresponding to
> > (iat1-iat2) and (iat2-iat3) or (iat1-iat2) and (iat3-iat2).
>
> The latter; it would be what you would get for an angle defined by three
> single atoms iat1, iat2 and iat3. But be sure to run some simple tests
> with
> known geometries, to make sure you are getting the restraint you want.
>
> ...dac
>
>
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Received on Mon Dec 30 2013 - 14:00:03 PST
