AMBER Archive (2004)

Subject: AMBER: gaff parameter ambiguities

From: Anthony Fejes (fejes_at_zymeworks.com)
Date: Wed Nov 03 2004 - 17:16:07 CST

Hi,

I believe I have the latest AMBER force field (AMBER 8) which includes
the file gaff.dat.

This file includes duplicate non-identical entries for a number of
bonds. Can anyone explain why this is, or even better, does anyone know
which entry is correct?

For instance, from the first section: (excess spacing removed for
clarity)

cc 12.01 0.360 Sp2 carbons in non-pure aromatic systems
cd 12.01 0.360 Sp2 carbons in non-pure aromatic systems, identical to cc
...
cg 12.01 0.360 Inner Sp carbons in conjugated systems
ch 12.01 0.360 Inner Sp carbons in conjugated systems, identical to cg
...

I would expect the entries for cc-cd in bonds to be the same as for cd-
cd, and cc-cc, however, the following entries exist:

...
cc-cc 418.3 1.429 SOURCE1 740 0.0058 0.0069
cc-cd 504.0 1.371 SOURCE3 523 0.0156 0.0217
...
cd-cd 418.3 1.429 SOURCE1 740 0.0058 0.0069
cd-cd 504.0 1.371 SOURCE3 523 same as cc-cd
...

Does SOURCE3 replace SOURCE1?

Even more confusing, the ch-ch duplicates both cite the same source:

...
ch-ch 494.2 1.377 SOURCE1 42 0.0000 0.0000
ch-ch 949.5 1.191 SOURCE1 80 same as cg-ch
...

could anyone shed some light on this for me?

Anthony Fejes

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