How can I make the .hdb(hydrogen data base) entry for new molecule ?

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Ricardo J Ferreira

Hi,

you are using an united-atom force-field. "HA" does not exist the GROMOS force-field.

Subhamoy Mahajan

Similar to the .rtp definitions, "-[name]" (for exmaple -C in your case) means atom [name] of the previous residue. Similarly "+[name]" means atom [name] for the next residue.

Look at https://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html for hydrogen type.

Hope this helps.