AMBER Archive (2007)

Subject: Re: AMBER: improper torsions

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Mon Jan 08 2007 - 13:45:09 CST


Can you paste your ATP pdb file and your prepin file?

Best regards.

Fenghui Fan

--- Ed Pate <pate_at_math.wsu.edu> wrote:

> 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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