Re: AMBER: HG atoms in CYX residues

From: Carlos Simmerling <>
Date: Fri, 26 Oct 2007 06:20:05 -0400

CYX do not have HG. CYS does. You need to either
delete the HG atoms or rename the CYX as CYS in your input
pdb. Make sure to check if there should be disulfide bonds-
where did the hydrogens come from?

On 10/26/07, francesco zonta <> wrote:
> Dear all,
> when trying to load a pdb file with xleap, it adds a new H atom for each
> CYX residue I have in the protein:
> Created a new atom named: HG within residue: .R<CYX 53>
> After that I check the protein with check unit command and the result is
> like this:
> Unit Editor: FATAL: Atom .R<CYX 53>.A<HG 11> does not have a type.
> How can I solve this strange problem?

Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail:
Stony Brook, NY 11794-5115          Web:
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Received on Sun Oct 28 2007 - 06:07:35 PDT
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