pdb2gmx can't form special bonds with terminal patched atoms
We have a system that requires a metal coordination to a C-terminal oxygen atom and therefore is represented with a covalent bond. No matter what we try,
pdb2gmx refuses to make this linkage. It seems as though the following is happening:
1. The .rtp and .tdb (residue + patch) entries are combined and atoms that are slated for removal or replacement are flagged in the hackblock structure. At this point, they're essentially in limbo.
2. Residue renaming occurs based on protonation state detection (e.g. HIS)
3. The specbond.dat matrix is processed and bonds are assigned
4. Atoms are renamed based on the hackblock and the final topology is written
The problem is, for this to work, steps 3 and 4 would have to be reversed. I don't know how complicated that would be to get working, because I know the
pdb2gmx code is a nightmare.
Files needed to reproduce the problem are attached. Command used:
gmx pdb2gmx -f 1rov_4pdb2gmx.pdb -o 1rov_gmx.pdb -p 1rov_gmx.top -ff charmm36-jul2017 -water tip3p -merge all