AMBER Archive (2008)

Subject: Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file?

From: David A. Case (
Date: Mon Jan 28 2008 - 10:11:02 CST

On Mon, Jan 28, 2008, Steve Spronk wrote:

> The problem lies in the fact that your PDB file has an atom called H in the
> CYM amide bond (which is the standard for every other amino acid residue),
> whereas LEaP is expecting an atom named HN (look at atom 5 of the library
> definition).

This will be fixed in the next release...thanks for catching that....dac

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