AMBER Archive (2004)

Subject: Re: AMBER: problems with extra points

From: German Sciaini (
Date: Fri Jun 18 2004 - 06:08:18 CDT

Thanks dac,
I will try to modify extre_pts, but thinking that is not easy... I became
an amber user a month ago and do not understand the code yet..., but I will
try to..
Thaks for all....

At 11:50 a.m. 16/06/2004 -0700, you wrote:
>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.
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