Charmm36 ff port has a missing dihedral for some N-terminal NH2 builds

User discussions
1

GROMACS version: 2022.2
GROMACS modification: No

Hello,

I’m not sure if this is the best place to report an issue with the charm ff gromacs port and its interaction with pdb2gmx, but it seems like a reasonable place to describe the behavior.

I downloaded charmm36-jul2021.ff.tgz from MacKerell Lab and ran pdb2gmx with gromacs 2022.2 on a protein with an N-terminal Glu. I selected the NH2 option for the N-terminus (“Start terminus GLU-1: NH2”). Eventual running of grompp complains that there is a missing proper dihedral, which is N/CA/CB/CG for the N-term Glu, which is types NH2/CT1/CT2A/CT2.

To solve this, I copied the NH3/CT1/CT2A/CT2 [ dihedraltypes ] entry from ffbonded.itp into my .top file and things work OK now.

For what it’s worth, this problem does not exist for the gromacs bundled charmm 27 ff (for which Glu CB is type CT2, not type CT2A). It is also not an issue for charmm36-jul2021.ff when using a NH3+ N-terminal Glu.

Thank you,
Chris.

2

This is the appropriate solution. FWIW, it’s not an issue with the C36 port specifically, but the fact that this specific dihedral is not in the CHARMM force field files themselves, so it’s just a situation that we didn’t anticipate people needing.