Re: [AMBER] unique atoms in TI softcore

From: case <>
Date: Fri, 18 Oct 2013 11:07:47 -0400

On Thu, Oct 17, 2013, Hannes Loeffler wrote:
> Not quite I'm afraid because I still don't know what you mean by
> "unique". I tried to explain my thoughts in my previous email but
> maybe I was not clear.
> Maybe you mean scmask should contain only those atoms which are absent
> in the respective other parm file and thus could also be just defined
> explicitly as dummy atoms (as for the second TI implementation that is
> supported in Amber12). But why does the tutorial make H and O softcore
> atoms in the benzene to phenol transformation where H obviously becomes
> O: is that because the elements or atom types are different, or because
> they belong to a "group"?

The user can choose which atoms to be "unique" in several ways. This is
related to the "single topology" vs. "dual topology" choice. I don't have
enough experience with these transformations to know which is better for
the example of phenol to benzene -- my feeling is that dual (OH are unique
on the phenol side, H unique on the benzene side) sounds better. But the
choice is a choice, and is unrelated to groups or atom types.


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Received on Fri Oct 18 2013 - 08:30:04 PDT
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