GROMACS version:2024.1
GROMACS modification: No
I am running a simulation on a protein that requires a cation and coordinating water molecules to be bound. For reference I am using the charmm36-July2022 forcefield and had the water molecules identified as TIP3P. During the pdb2gmx step, when i attempt to input a coordinate file that has my protein, 2 ions and 4 water molecules within it, I got an error that 8 atoms will be missing from my protein molecule but i can use the incomplete topology using the -missing option. (the 8 molecules referred to the 2H’s per 4 water molecules.
I went ahead and ran it with the -missing command. I received the following note and warning for each of the water molecules in my coordinate file:
"atom H1 is missing in residue TIP3 759 in the pdb file
atom H1 is missing in residue TIP3 759 in the pdb file
You might need to add atom H1 to the hydrogen database of building block TIP3 in the file solvent.hdb (see the manual)
You might need to add atom H1 to the hydrogen database of building block TIP3 in the file solvent.hdb (see the manual)
atom H2 is missing in residue TIP3 759 in the pdb file
atom H2 is missing in residue TIP3 759 in the pdb file"
“WARNING: WARNING: Residue 663 named TIP3 of a molecule in the input file was mapped to an entry in the topology database, but the atom H1 used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.”
My question is, how can i edit the solvent.hdb file of the charmm36 forcefield to include H1 and H2 for each water molecule. The only molecule represented per water molecule is OH2 in my .gro file.
My second question is, where else within the forcefield will i have to update to include these changes?
Thanks in advance for any help!