AMBER Archive (2004)

Subject: AMBER: Assignment of parameters, missing parameters

From: Julien Michel (
Date: Mon Mar 22 2004 - 09:47:15 CST

Dear Amber users,

        I would like to report that Leap can assigns torsions incorrectly when
generating a prmtop file. The problem seems to be caused by atom typing.
How is it possible to differentiate the following torsion ca-ca-ca-ca in a
phenyl ring and ca-ca-ca-ca in a biphenyl(GAFF atom types) ? As it currently
stand, with AMBER7, leap does not make a difference between the torsion
linking the two phenyl rings and the'usual' torsion and incorrectly assign a
wrong torsion. The OPLS forcefield has two different torsions in this case (the
torsion around the bond linking the two phenyls rings has a smaller amplitude,
faciliting ring rotation), while I can only locate the torsion X-ca-ca-X in
gaff or(X -CA-CA-X in AMBER). Even if I were to generate parameters for the
missing torsion, how would I force leap to recognize it ? Manually editing the
prmtop file, even with scripts, is certainly not practical.
        The best solution might be to introduce a new atom type for
something like "aromatic sp2 carbon linked to another atom not in the ring
which has more than one bond". I do not have AMBER8, and I would like to know
if leap/GAFF2 can handle this case ?

Julien Michel
University of Southampton
Department of Chemistry
Dr J. W. Essex group 
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