GROMACS modification: No
I am adding a new protein residue to the CHARMM36 forcefield (July 2021). As per the instructions in the GROMACS manual (“Adding a Residue to a Force Field”), I modified residuetypes.dat, aminoacids.rtp, and aminoacids.hdb with the new residue entry. It seems that all bonds in the residue already exist in the forcefield.
After I execute pdb2gmx and select CHARMM36 with the updated TIP3P water model, I receive the following output:
Opening force field file ./charmm36-jul2021.ff/atomtypes.atp
Reading residue database… (Charmm36-jul2021)
Opening force field file ./charmm36-jul2021.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2021.ff/carb.rtp
Opening force field file ./charmm36-jul2021.ff/cgenff.rtp
Opening force field file ./charmm36-jul2021.ff/ethers.rtp
Opening force field file ./charmm36-jul2021.ff/lipid.rtp
Opening force field file ./charmm36-jul2021.ff/metals.rtp
Opening force field file ./charmm36-jul2021.ff/na.rtp
Opening force field file ./charmm36-jul2021.ff/silicates.rtp
Opening force field file ./charmm36-jul2021.ff/solvent.rtp
Opening force field file ./charmm36-jul2021.ff/aminoacids.hdb
Program: gmx pdb2gmx, version 2022.2
Source file: src/gromacs/gmxpreprocess/h_db.cpp (line 180)
Error reading from file ./charmm36-jul2021.ff/aminoacids.hdb
When there is a problem with the .hdb file format, I am notified of the formatting error, which suggests that the command can access the file, so it’s not a permissions issue. I’ve formatted the new entry exactly as the others in the .hdb file.
Could anyone suggest the origin of this error and/or how I might go about solving it? I can provide the new entries, or any other information, if needed. Thank you for your time.