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

Qinghua Liao scorpio.liao at gmail.com
Wed Aug 9 14:53:39 CEST 2017

Dear Justin,

Thanks very much for your suggestion, it works well now.

All the best,

On 08/09/2017 01:28 PM, Justin Lemkul wrote:
> 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

More information about the gromacs.org_gmx-users mailing list