Re: amber-developers: Implicit Solvent and dummy atoms

From: David A. Case <>
Date: Sat, 2 Sep 2006 09:08:21 -0700

On Thu, Aug 31, 2006, Ilyas Yildirim wrote:
> I am trying to make some changes in the AMBER code to use implicit solvent
> in structures which have dummy atoms in it.

In the loops that compute the effective Born radii, you probably just want to
put in a test to skip the dummy atoms. You could identify these by their
name, or by having both a zero charge and and zero radius (or by some other
criteria. It may also be required to modify the energy loops to again skip
some atoms, but I'm not sure about that.

...good luck....dac
Received on Sun Sep 03 2006 - 06:07:26 PDT
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