[gmx-users] Atom OXT in residue was not found

[Justin Lemkul]

On 8/9/17 7:21 AM, Qinghua Liao wrote:
> Hello,
> 
> I want to simulate a protein with a ligand (small molecule, 15 atoms). But I 
> have problem of generating the topology file.
> I added the topology of the ligand as a new residue in force field database 
> (aminoacid.rtp), but I got the error when I run pdb2gmx
> interactively with -ter and chose none for the ligand:
> 
> Atom OXT in residue DH2 495 was not found in rtp entry DH2 with 15 atoms
> 
> The problem is that there isn't any atom named OXT in the ligand. I also 
> searched the mailing list, someone mentioned that
> pdb2gmx might rename the atom name of the atoms in the ligand. I don't 
> understand why pdb2gmx complains something like this
> when the atom is not in the ligand. Any suggestions? Thanks a lot!
> 

pdb2gmx is trying to apply C-terminal protein patching to your ligand.  If you 
have listed DH2 in residuetypes.dat as Protein, don't.  Also note that atom 
names are translated via xlateat.dat so if you have one of those atom names, and 
DH2 is considered a protein residue, you need to choose a different atom name.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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