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

Qinghua Liao scorpio.liao at gmail.com
Wed Aug 9 13:24:58 CEST 2017


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!

All the best,

More information about the gromacs.org_gmx-users mailing list