On Thu, Apr 03, 2003, Dr.K.Veluraja wrote:
> We are using Amber7 (Sander) for our energy minimization
> calculation. Our interest is to study the substrate-protein interaction
> which is dominated by mainly hydrogen bonds. But we do not know whether the
> Amber7 version (Sander) takes care of the hydrogen bonds. If not, is there
> anyway to incorporate hydrogen bonding interactions in the input data.
Hydrogen bonding effects are indeed included in all of the standard Amber
force fields. See the papers cited in the Users' Manual for an explanation
of how these were developed and tested.
...good luck...dac
--
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David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Apr 03 2003 - 18:53:01 PST
