Hydrogen database .hdb file

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1

GROMACS version: 2020.1
GROMACS modification: No
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Is there some program or script to create an new entry for a new molecule in the hydrogen database .hdb file? I read the manual, but it still a hard task to do manually…

Thanks in advance

2

AFAIK there are none, it’s both a highly system-specific task (many things to detect/assume) and one that isn’t done too frequently, usually when people create many new molecules they don’t need to add .hdb files. If you were to generate that from an .rtp or .itp, there is no easy way to guess the geometry in a foolproof manner, while .pdbs for small molecules usually have provisional atom names.

What is your specific case? Maybe there’s another way around this.

3

I think I got it. So, some script could use a corrected .pdb file to generate .hdb file, but If pdb has correct H’s name its unnecessary to generate such hydrogen database. My specific case was SDS molecule that hasn’t .hdb entry in CHARMM27 ff, lipids.hdb is an empty file. But it has in 36 version, so I just copy the entry to the right file.
Thank you.