AMBER Archive (2007)

Subject: Re: AMBER: improper torsions

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jan 08 2007 - 14:00:06 CST

> I am tring to simulate an ATP analog. I generated the .prep file using
> antechamber. The analog has a ring structure hanging of the ribose, with
> several sp2 atoms in the ring. When I look at my leap.log file, there are
> several warning statements "No sp2 improper torsion term ..." for the sp2
> atoms in the ring, plus one for the adenine ring itself. They were not
> generated by antechamber. Does the warning indicate that amber has
> recognized the problem and fixed it, or do I need to include them in
> my .prep file?

Including them in the prep file has no effect except to provide
a comparison with how many impropers leap applies. Leap ignores
prep impropers and tries to find an improper term to match each
atom with 3 bonds. If the forcefield has no such term, none is
applied.

Bill
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