AMBER Archive (2009)

Subject: Re: [AMBER] file contains 2 atoms not in residue templates

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun May 24 2009 - 08:12:14 CDT

On Sat, May 23, 2009, Workalemhu Berhanu wrote:
>
> When I was loading a pdb file with the amino acid sequence of two
> strands of mvggvv I got in xleap that file contains 2 atoms not in the
> residue template. I am using amber9. When I examined my molecule I found
> out there are two sulfur atoms from the methionine amino acid. Can
> anyone help me in fixing my problem?

> Loading PDB file: ./mvggvv.pdb
> Created a new atom named: OT within residue: .R<CVAL 6>
> Added missing heavy atom: .R<CVAL 6>.A<OXT 17>
> Created a new atom named: OT within residue: .R<CVAL 12>
> Added missing heavy atom: .R<CVAL 12>.A<OXT 17>

The terminal carboxylate oxygens in your pdb file are named "OT" when they
should be named "OXT". I don't see any evidence of problems related to sulfur
atoms in the output you posted; but please make sure that the pdb file is
correct (i.e. has only one sulfur atom per methionine.)

...dac

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