Re: [AMBER] Adding a Dummy Atom to Benzene

From: David A Case <>
Date: Fri, 21 Oct 2016 08:19:06 -0400

On Thu, Oct 20, 2016, Samuel Walpole (PHA) wrote:

> Thank you for your reply. I've read that this can be achieved by
> considering the dummy atom as an 'extra point', such as the extra point
> in TIP4P water. How would I define my dummy atom as an extra point in
> leap? The documentation doesn't seem to go into this.

Amber supports only certain types of extra points, that are hard coded into
the code (e.g. the define_frames() routine in extra_pts.F90 in sander.) You
would have to grok this code (there are comments, but no formal
documentation), then add a new section.

What are you trying to do with this point? Note that you can generate
restraints (extra FF terms) that refer to the center of mass of the benzene
ring. Maybe that will serve your needs(?)


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Received on Fri Oct 21 2016 - 05:30:04 PDT
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