Error when adding new residue to hdb (CHARMM36) – User discussions

GROMACS version:2022.2
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)

Fatal error:
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.


Please provide the details of everything you changed in the files. Make sure you’re using a plain-text editor and you don’t have any weird line endings (use dos2unix if needed).

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