Error when adding new residue to hdb (CHARMM36)

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1

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.

2

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).

3

I’ve attached a .txt file with the entries I added (modifications.txt). I created it in a plain-text editor (Notepad) and there shouldn’t be anything strange about the lines.

For clarity, I also added the modified .hdb, .dat, and .rtp files.

https://drive.google.com/drive/folders/1FsH3fSlGW7j63Ee7JdjXvCYIGvCZtDF0?usp=sharing

4

The problem is that you specify 10 lines for the .hdb entry but there are 11. This causes the file to be parsed incorrectly.