AMBER Archive (2007)

Subject: AMBER: improper torsions

From: Ed Pate (pate_at_math.wsu.edu)
Date: Mon Jan 08 2007 - 13:08:36 CST

Dear Amber community:

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?

Thanks for the help.

Ed Pate
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