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.