Re: AMBER: ibelly in AMBER 6

From: David A. Case <>
Date: Fri, 17 Oct 2003 17:51:29 -0700

On Fri, Oct 17, 2003, Qing Zhang wrote:
> I want to use ibelly to only allow parts of a molecule
> to move (ibelly=1), and also use distance-dependent
> dielectric constant (igb=3). However, minimization
> does not work and shows an error message:
> "When igb>0, the moving part must be at the start of
> the molecule."
> Should the moving part be ONLY at the start of the
> molecule?


(I continue to think that using ntr=1 is generally a better way to restrain
parts of the system than to use the belly. And if no one steps up to improve
the implementation of the belly option, it will probably disappear in the next

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 - 02:53:01 PDT
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