Pdb2gmx error: "atom MW is missing in residue HO4" using charmm36-jul2022 with TIP4P water model

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hello,

I’m running GROMACS (version 2024) using the charmm36-jul2022.ff (of the MacKerell lab website with the TIP4P water model. When I run pdb2gmx, I consistently encounter the following error:

Fatal error:
atom MW is missing in residue HO4 [residue number] in the pdb file

As I understand it, TIP4P water uses a virtual site (dummy atom MW) that is defined in the force field topology (via a [ virtual_sites3 ] block) and is generated on the fly. The input PDB only contains the three atoms (OW, HW1, HW2) per water molecule.

Why does pdb2gmx complain about the missing MW atom in HO4 residues even though TIP4P is supposed to compute it virtually?

What might be wrong in the standard CHARMM36 settings that is causing this error, and how can it be fixed?

Any help or suggestions would be appreciated.

Thanks,
Emmanuel

2

Even if the site is virtual, the atom for GROMACS is real. The TIP4P model is a four point water model, so you need to solvate with a four point water model, like with gmx solvate -cs tip4.gro.

3

Thanks for the clarification. However, my issue isn’t about generating new TIP4P water molecules via solvation. I already have a PDB with waters, and I need to convert those existing waters correctly using pdb2gmx. Interestingly, using OPLSAA 2013 as the force field (with GROMACS 2021 version), the conversion works fine, but with CHARMM36 it fails with an “atom MW is missing in residue HO4” error. It seems that when using CHARMM36, pdb2gmx doesn’t properly generate the virtual MW atom from the existing water coordinates. Does anyone have suggestions on how to force the conversion of these pre-existing waters so that the dummy atom (MW) is correctly created, rather than having to resolvate the system?

Any insights would be appreciated!