AMBER Archive (2004)

Subject: Re: AMBER: Bond type in leap

From: Bill Ross (
Date: Thu Apr 22 2004 - 11:53:33 CDT

> when i load the saved pdb files in leap and use desc to get the
> description, it shows that C and O atoms of the peptide bond are joined
> with asingle bond instead of the double bond.

The bond order is only used when leap minimizes and there are no regular
amber parameters. It has no effect on the saved prmtop used by the rest
of amber.

> Initially when I loaded the peptide in leap it added 4 missing atoms:

This implies that leap may have converted a terminal residue to the amber
default, or that the basic residue definition differs between amber and
Insight. In this case, CGLYN is C-terminal, and OXT is added:

> Added missing heavy atom: .R<CGLN 10>.A<OXT 18>

The main problem here is leap adding an unrecognized atom from the pdb:

> Created a new atom named: H within residue: .R<NGLN 1>
> FATAL: Atom .R<NGLN 1>.A<H 20> does not have a type.

This could be because of an atom naming difference. The simplest approach
is to delete the offending H from the pdb file.



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