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
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
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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
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