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
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
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