[gmx-users] Definiting protonation in pdb2gmx input

mhuhtala at abo.fi mhuhtala at abo.fi
Mon Apr 16 15:44:32 CEST 2018

Quoting Justin Lemkul <jalemkul at 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  

More information about the gromacs.org_gmx-users mailing list