Error while working with ADP as a cofactor

User discussions
1

GROMACS version: 2021
GROMACS modification: Yes/No

Dear GROMACS users,

I am trying to run a MD for a complex containing a protein, a ligand, ADP and Mg2+ ions. charmm36-feb2021 force field has been employed.

[assuming that like ATP, the parameters for ADP are also predefined in charmm36-feb2021]

This is the error I am getting:

Program:     gmx pdb2gmx, version 2021.2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)

Fatal error:
Atom H01 in residue ADP 355 was not found in rtp entry ADP with 39 atoms
while sorting atoms.

For a hydrogen, this can be a different protonation state, or it
might have had a different number in the PDB file and was rebuilt
(it might for instance have been H3, and we only expected H1 & H2).
Note that hydrogens might have been added to the entry for the N-terminus.
Remove this hydrogen or choose a different protonation state to solve it.
Option -ignh will ignore all hydrogens in the input.

We also tried -ignh, which worked for ATP but not in this case.

One observation is that ADP is mentioned in merged.rtp file but not in merged.hdb file. Could this be the reason for this error?

Any help will be greatly appreciated.

Regards,
Hemant

2

Atom names have to match .rtp entries. The -ignh option only works if there is a corresponding .hdb entry to reconstruct the missing H atoms. Use the newest version of the CHARMM36 port (July 2021), where we have addressed this and have an .hdb entry for ADP.

3

Thank you Justin. It worked.

Looks like in the July-2021 version of charmm36, the atom names for the chloride and sodium ions have been changed (from CL to CLA and NA to SOD).

4

SOD and CLA are standard CHARMM nomenclature and therefore should be used with the CHARMM36 force field. We previously wrote the ion topologies manually, but as part of the new, automated conversion, we don’t. The automated approach is preferred to avoid issues that may arise when things change, though ions haven’t changed in many years.