[gmx-users] Definiting protonation in pdb2gmx input

[Justin Lemkul]

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 
functional).

> 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

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

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