On 4/16/18 9:44 AM, mhuht...@abo.fi wrote:
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.

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

303 Engel Hall
340 West Campus Dr.
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jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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