AMBER Archive (2009)

Subject: RE: [AMBER] Warning: No sp2 improper torsion term for

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 05 2009 - 09:13:53 CDT

Hi Alan,

> Building improper torsion parameters.
> ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
> atoms are: CG CE2 CD2 CE3
> ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
> atoms are: NE1 CZ2 CE2 CD2

This is just warning you that atoms CG and NE1 are sp2 but do not have an improper torsion on them to keep them planar. This is not necessarily wrong, not all sp2 type atoms have to have improper terms since other factors, such as angles etc will act to keep them planar. Leap just thinks that because the atom is sp2 it should have an improper term. In short it is just a warning and there is no need to worry about it.

All the best
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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