Error with pdb2gmx when peptide is capped

User discussions
1

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.

2

Hi,
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
Alessandra

3

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.

4

Hi,

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.

5

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.

6

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.