AMBER Archive (2009)

Subject: [AMBER] gaff.dat questions

From: gilbert_at_bluemarble.net
Date: Wed Sep 09 2009 - 09:02:28 CDT

I found a duplicate entry for the cd-cd bond in gaff.dat

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

Is this an error or is there something in code (ie a bond order test) to pick one.

Also the torsion data has a large number of entries with a barrier height of
0.0. Are these just place holders to be updated at some future time or does the
amber prep code not zero out all torsions for which there are no data. Since
these torsions don't contribute to the rotational barrier why include them in
the parameter file.

Kevin Gilbert
Serena Software

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