AMBER Archive (2007)

Subject: Re: AMBER: HG atoms in CYX residues

From: David A. Case (case_at_scripps.edu)
Date: Fri Oct 26 2007 - 10:28:36 CDT

On Fri, Oct 26, 2007, francesco zonta wrote:

> 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>

Just to add to what Carlos said: the LEaP message above is a little
misleading. The HG atom is already (mistakenly?) in your pdb file. Since HG
is not in the CYX residue template, LEaP "creates" (adds) this atom to the
residue.

As Carlos said, you need to figure out whether these residues are really CYS
or CYX, and edit the pdb file.

...good luck...dac

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