[gmx-users] Defining protonation in pdb2gmx input

Justin Lemkul jalemkul at vt.edu
Wed May 9 16:03:14 CEST 2018

On 5/9/18 9:11 AM, mhuhtala at abo.fi wrote:
> This is continuing a thread from a month ago.
>> Quoting Justin Lemkul <jalemkul at vt.edu>:
>>> 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 
>> functional).
> Reading the source code of pdb2gmx, that does not seem true. I don't 
> fully understand the code after a quick look, but it seems to me that 
> ASPH and GLUH are always matched to ASP and GLU (if not entered 
> manually), and that the protonation routine is only for HIS. And once 
> pdb2gmx matches ASPH with ASP, it refuses to read the hydrogen atom 
> even if it is in the input (because it wants ASP).
>>> 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.
> That's not true, actually, as far as I can tell. I did a bit more 
> testing, and ASPH in the input does NOT get protonated for AMBER99 or 
> CHARMM27 either. I tried with 2018.1.

AMBER uses ASH and CHARMM uses ASPP. Both of those work; I just 

> The bug I reported earlier (assuming then it was Gromos only): 
> https://redmine.gromacs.org/issues/2480
There is a problem in automatically detecting provided ASPH, and it 
affects OPLS-AA, too. The topology is correctly written if interactively 
selecting the protonation state via -asp (I confirmed this with both 
OPLS-AA and GROMOS) but otherwise does not work. That may be useful 
information in updating the bug report.



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

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129


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