AMBER Archive (2009)

Subject: [AMBER] Non-planarity of amide atoms after optimization

From: Sanghwa Han (hansh_at_kangwon.ac.kr)
Date: Wed Jan 07 2009 - 21:17:18 CST

Dear Amber users,

 

In Biochemistry textbooks, an amide bond (NH-CO) in a peptide is planar.

But when I optimize a capped amino acid (e.g. ACE-Amino Acid-NME) the
dihedral HN-CO often becomes smaller than 180 degrees (say, 165 degrees).

Do I need to constrain the HN-CO to 180 degrees to obtain an optimized
structure that is used in a RESP charge derivation.

 

Thanks.

 

Sanghwa Han

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