On Sat, Nov 15, 2003, Giulio Rastelli wrote:
>
> 2) time ago I posted an example of mm_pbsa calculation which used the
> gaff force field and mgbjsb radii, that assigned a radius of zero to the
> first atom in the prep file of the ligand. After many tests, I am pretty
> inclined to say that there is a bug in the code for assignment of mgbjsb
> radii to gaff-atom types (the atom type which had a zero radii was the
> carboxyl oxygen o, nothing strange). Bugfix 24 was meant to solve a few
> problems regarding lower-case atom types in gaff, and to account for
> mbondi radii. I wonder if anybody could also check the code where mgbjsb
> radii are read, that would be great!.
Note that Jayaram et al. defined their GB parameters for the Amber atom types
and charges. It is not clear how one should "extend" their work to a
different force field, or if it would their "their work" any more....
If you want to play with this, modify the code around line 5213 of unitio.c
(in $AMBERHOME/src/leap/src/leap) to recognize lower case atom types. Or,
just manually edit the prmtop file to put in the radii you want.
> 3) mbondi radii in mm_pbsa work fine, but as far as I understand,
> mm_pbsa was tested only for mgbjsb radii to be used with igb=4.
There is no reason to suppose the other variants of gb would not work as
well as the mgbjsb parameters for mm-gbsa calculations, at least as far as
I know. GB methods have been worked on so that GB and PB give broadly similar
results for the same sets of charges and atomic radii. The question of the
"best" radii (in terms of physical realism) is still very much an area of
research.
...hope this helps...dac
--
==================================================================
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 Sat Nov 15 2003 - 18:53:01 PST
