Quoting Justin Lemkul <jalem...@vt.edu>:

I just tested this in GROMACS 2018 and it works fine - if you provide
the protonated residue name, pdb2gmx correctly interprets the
protonation state. Do you have a use case that fails?

Is this behavior documented somewhere? I don't seem to find any mention of it.

My initial problem was that when I attempted to use a structure with hydrogens (polar only) as input, I just got a lot of error messages about atom names and the numbers of atoms not matching the residue topology, which made me assume that pdb2gmx simply does not do the trick.

Now I did a bit more testing, and at least renaming ASP to ASPH in the input will get me an ASPH in the output, but only the residue name, not the hydrogen. So I get a residue named ASPH, but the structure is an unprotonated ASP. Is this a bug? Or is pdb2gmx expecting to find the hydrogen atom line in the input?

Then I tried changing a HIS to HISA, and that one works. By default, pdb2gmx adds two hydrogens to that histidine, but with HISA specified, I do get only the hydrogen on ND, as expected.

This is all using Gromacs 2018 and specifying GROMOS96 54a7, and modifying a crystal structure PDB file taken from the PDB, with no hydrogens.




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