Error with pdb2gmx when peptide is capped

GROMACS version: 2018.3
GROMACS modification: No

I created a peptide (7-residue long) and capped it such that ACE-(peptide)-NME.
When I ran the pdb2gmx (gmx pdb2gmx -f peptide.pdb -o peptide.gro -ignh -ter), I got an error saying, Atom X in residue YYY not found in rtp entry, so I fixed the problem by changing the atom’s name to whatever is compatible with the force field (CHARMM36-m).

But this time I get another error: Residue 9 named NME of a molecule in the input file was mapped to an entry in the topology database, but the atom CH3 used in that entry is not found in the input file…

I do have the CH3 in my PDB file. Can anyone help me with this problem? Thanks.

As far as I understood you have defined the termini in your peptide with a specific entry in the rtp file (e.i NME). In this case you do not need the option -ter. Did you try to run without the option -ter ?
Best regards

The NME residue definition in the CHARMM36 port for GROMACS is not fully consistent with an input coordinate file generated by CHARMM, which will have CAT instead of CH3. I will rectify this in a future version of the port but for now the solution is to change the atom name(s) in the input coordinates to match the .rtp entry for NME.


Thank you for the reply. When I didn’t include the option “-ter”, I got Atom N in residue 1ACE not found in rtp entry. pdb2gmx automatically tried to look for or add NH3+ to the ACE and COO- to the NME.

But first of all my ACE is 0ACE, not 1ACE. Secondly, the ACE doesn’t have any N atoms.

Thank you for the reply.

I think it’s working now. I changed all the names of the atoms of my NME to match those in the .rtp entry, and I am now at the MD production step without any errors.

And it seems the “-ter” option is necessary in the pdb2gmx, especially when I am dealing with a capped peptide.

The CHARMM36 force field always requires the explicit use of -ter since there are not separate .rtp files for protein and nucleic acid residues. This is a consequence of how we have to do the file conversion.