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!


All the best,
Qinghua


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