AMBER Archive (2002)

Subject: gaff and parm99

From: Pascal Bonnet (pascal.bonnet_at_man.ac.uk)
Date: Wed Jul 24 2002 - 08:11:36 CDT

Hi,

I have two questions:

1)
I found in the manual of AMBER 7 about ANTECHAMBER this sentence (page
83):

Hence, it is generally expected that you will use one of the Amber force
fields to describe
your protein or nucleic acid, and the gaff.dat parameters to describe
your ligand; as mentioned
above, gaff.dat has been designed with this in mind, i.e. to produce
molecular mechanics descrip-tions
that are generally compatible with the Amber macromolecular force
fields.

In GAFF (general amber force field) the carbon radius is 1.7 A and in
parm99 is 1.9080 A (and 1.5 and ~1.7 for oxygen radius)
I don't think it is coherent to use two different force fields in the
same system receptor-ligand?

Any suggestions?

2)
Why in GAFF, the hydrogen radius of TIP3P model is 1.2 and not 0 as in
parm9X?
RADIUS HW 1.2 (from GAFF)
HW 0.0000 (from pam99)

pascal
  

-- 
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 Dr. Pascal Bonnet
 School of Pharmacy and Pharmaceutical Sciences,
 University of Manchester, Oxford Road,
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 Tel:(+44) (0)161 275 2431
 http://www.man.ac.uk/~mbpsspb3