AMBER Archive (2009)

Subject: Re: [AMBER] H-Bonds

From: Thomas Cheatham III (
Date: Wed Mar 04 2009 - 15:00:30 CST

> What do I need to put in my file to pick up a serine side chain
> O-H proton as a donor and an aspartate carboxyl group as an acceptor? I
> tried using "acceptor: ASP COO" but that didn't work. As for the serine
> side chain O-H proton I have no idea what to do.

donor ASP OD1
donor ASP OD2
acceptor SER OG HG

When coding I flipped convention to electron pair donor and electron pair
acceptor rather than H-donor/acceptor. Key for specification is residue
name, atom name. With the mask keyword you can use masks.


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