[gmx-users] Definiting protonation in pdb2gmx input

Justin Lemkul jalemkul at vt.edu
Mon Apr 16 17:07:44 CEST 2018

On 4/16/18 9:44 AM, mhuhtala at abo.fi wrote:
> 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.

It's always been default behavior - if pdb2gmx matches a residue name, 
it processes the coordinates according to the .rtp file.

> 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.

As you mention below, you're using a UA force field, which won't have 
most of the H atoms you are supplying, so you'll get errors. Using -ignh 
should fix that (but then again, see below).

> 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?

All necessary hydrogens should be reconstructed according to the .hdb 
file (for which entries for protonated amino acids exist and are 

> 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.

There does appear to be a problem specifically with united-atom force 
fields. Both CHARMM and AMBER function correctly, with or without -ignh. 
Using any GROMOS variant, with or without -ignh leads to a problem. 
Please file a bug report on Redmine and include example input files and 
pdb2gmx syntax you're using.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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