AMBER Archive (2004)

Subject: AMBER: turning off HB interactions

From: Taner E. Dirama (
Date: Tue Aug 17 2004 - 15:12:34 CDT

Dear All,

I would like to look at the effect of hydrogen bonds on the dynamics of a
protein due to the surrounding solvent. I am wondering if there is a way to
turn off hydrogen bond interactions that are included implicitly in the van der
Waals term? If not, does it make sense to replace hydrogen bond capable groups
(or atoms) in the solvent molecules with similar ones, but those can not form
hydrogen bonds?

Thanks, in advance for any suggestions.

Taner E. Dirama
Department of Polymer Science 
The University of Akron
Akron, OH
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