AMBER Archive (2008)

Subject: AMBER: to understand GAFF: about A and B coefficients

From: Alan (alanwilter_at_gmail.com)
Date: Tue Jun 17 2008 - 11:42:34 CDT

Dears,
I used antechamber/leap from amberTools 1.0 to generate prmtop for a
benzene. This very simple example is an exercise to understand the prmtop
file format and the GAFF forcefield.

For a benzene, I have 12 atoms (H and C) and only 2 atom types: 'ha' and
'ca' according to GAFF nomenclature.

I am following http://ambermd.org/formats.html as much as possible. There,
one may find that B coef is also called C (topic 10C). C is also as it
called in 'rdparm' output. Whatever it is I am assuming B = C.

I understand that there would be 3 different parameters for LJ since I would
have interactions ha-ha, ca-ha and ca-ca. So in:

%FLAG LENNARD_JONES_ACOEF

%FORMAT(5E16.8)

  5.71629601E+03 7.62451550E+04 8.19971662E+05
%FLAG LENNARD_JONES_BCOEF

%FORMAT(5E16.8)

  1.85196588E+01 1.04660679E+02 5.31102864E+02

I see values for coef. A and B. However, in amber10/dat/leap/parm/gaff.dat
what one sees is (radius in Ang. and pot. well depth in kcal/mol):
ha 1.4590 0.0150
ca 1.9080 0.0860

I know there's a relation between those values, but I couldn't deduce or
find it in amber manuals.
So, in the end, I would like to know how can one get A and B values from
radius and pot. well depth. Also, how are they related to sigma and
epsilon.

I can't also find any information about '%FLAG RADII' means, since the
values I got in prmtop are different from radius in gaff.dat.

Many thanks in advance.
Cheers,
Alan 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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