PDB2GMX residue issues

User discussions
1

GROMACS version: Bioinformatics Reviews compilation
GROMACS modification: No

Dear forum,

I have the a pdb file, which I can convert to .gro using gmx editconf. Then, I would like to get .top by using PDB2GMX. However, the residues ROH and GB are not known and I cannot make .top. I tried to replace these with ABU which I know is in the residue file of Gromacs, However, that did not work. What should I do? The .gro file is easily visualized in VMD, so I know that this step works. Also GB and ROH residues are in the pdb and gro file, so I don’t understand why Gromacs is complaining as the names are in my opinion generic. Kind regards, Jonathan

2

I’m assuming you’re running into this issue:
https://manual.gromacs.org/current/user-guide/run-time-errors.html#residue-xxx-not-found-in-residue-topology-database

pdb2gmx can only write topologies for species it knows. What are ROH and GB?

What does this mean? You constructed ABU residues in their place, or you tried simply renaming the residues? The latter is certain to fail, but you haven’t told us what “didn’t work” means.

We’ll need more detail to help, including actual explanations of what manipulations you’ve done, exact commands and full screen output from pdb2gmx.