Re: AMBER: ibelly in AMBER 6

From: David A. Case <>
Date: Sat, 18 Oct 2003 09:48:16 -0700

On Fri, Oct 17, 2003, Qing Zhang wrote:
> I hope the belly option can be improved because it
> will make computational cost much cheaper, especially
> for large systems with small interesting parts, such
> as ligand docking, protein tails. While restraints do
> not reduce computational cost.

Note that the above statement is only true for pairwise potentials, and
hence is not directly applicable to either PME or GB, which are the two
main types of force field used in Amber.


David A. Case                     |  e-mail:
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            |
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Received on Sat Oct 18 2003 - 17:53:01 PDT
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