Re: IGB =4 with GAFF and bugfix24 incomplete?

From: David A. Case <>
Date: Wed 16 Oct 2002 11:55:24 -0700

On Wed, Oct 16, 2002, Tom Bishop wrote:
> However i'm having problems specifically w/ IGB=4 and GAFF.

The Jayaram, Sprous and Beveridge parameters implemented with igb=4 were
parameterized for the 1994 Amber force field; it is not clear whether or not
they would do a good job with the GAFF force field. Just making the
assignments case insensitive is probably not the right way to are
welcome to try it out, but this would go beyond what the authors of the
original paper had in mind, and the GAFF atom types are not simply the lower
case analogues of the parm94/99 atom types.

Of course, we should flag this combination, and put in a good error message
explaining that the combination is not (yet?) supported. Holger: can you
get this into the amber8 tree? (same for igb=3 and gaff).

The general question of "what GB paramters should one use with GAFF for
arbitrary ligand molecules" is pretty much unanswered, at least as far as
the published literature goes (although some papers on this subject are in
preparation). Arguably, the radii used with igb=1 or 2 are generic enough
(they mainly just depend upon atomic number) that reasonable results should
be obtained with GAFF. But this too would be an extension that has not yet
been tested very much, so users should be careful.

..hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Oct 16 2002 - 11:55:24 PDT
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