Wrong topology update after genbox solvation
I have a system with one protein chain, a ligand and 3 important tip4p water molecules near the active site, with residue names "HO4" in the .gro file and listed as "SOL 3" in the .top file.
I solvated my system with genbox, adding, say, 10000 water molecules. These are properly added to the .gro file with residue name "SOL".
Here comes the problem:
When genbox updates the .top file I expected it to either append the newly generated water molecules as "SOL 10000", or to update the present SOL entry to "SOL 10003" in order to match the total number of waters present.
What happens though is that genbox appends a new SOL entry to .top: "SOL 9997" so that now the total number of SOL molecules matches only the number of newly generated waters, regardless of the fact that there were already 3 present.
This creates an inconsitency in atom numbers in .gro and .top that is detected by grompp.
It is rather an inconvenience than a bug, but on a calm day you might consider changing the behaviour of genbox as it might save some users some time.
#2 Updated by Oliver Schillinger about 7 years ago
Renaming the residues to SOL seems to resolve the problem.
The residue names had been generated by pdb2gmx from a pdb structure.
I liked it at first as I can then refer to only these 3 waters I kept from the PDB as "resname HO4" in vmd.
I guess that's where the inconsistency stems from.