AMBER Archive (2004)

Subject: Re: AMBER: problems with extra points

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 16 2004 - 13:50:05 CDT

On Wed, Jun 16, 2004, German Sciaini wrote:
>
> >
> > My name is German, I am using Amber7 to try to simulate a 216
> >ammonia box.
> >The model for ammonia molecule is very similar to tip4p for water, also
> >rigid, but having one more site.

> > EXTRA_PTS: too many nghbrs!!

The types of extra points are hard-wired into the code; sander has to know
how to place the extra point relative to the other "real" atoms, and this
information is deduced from the types of bonds connected to the atom to which
the extra point is bonded.

Hence, to come up with a new type of long-pair (e.g. for ammonia), you would
have to modify extra_pts.f to recognize your new situation. Since there is
no full documentation of this, you will have to add a new case by analogy
to what is already there.

...regards...dac

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