[gmx-users] pdb2gmx: how to preserve original ions?

Justin Lemkul jalemkul at vt.edu
Wed Jul 18 03:26:23 CEST 2018

On 7/17/18 9:22 PM, Anderson, Amos wrote:
> Hi Gromacs users,
> I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for…
> I want to write a python script to prepare an arbitrary pdb for use with gromacs (e.g., does these steps http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html for the user). The input pdb to my script may have waters, ions, and ligand(s) in it already. In the tutorial it says "you are going to want to strip out the crystal waters, PO4, and BME. Note that such a procedure is not universally appropriate (i.e., the case of a bound active site water molecule).” The wording maybe implies that other than active site waters and the ligand of interest, I’d never want to preserve HETATOMs in my input file?
> If not, and if I do want to keep them, how do I? Do I just treat all of them like ligands in the tutorial, e.g., maybe a protocol like this (more precise for ions I care about)?
>       *   grep HETATOM my.pdb > hetatoms.pdb

HETATM, but yes.

>       *   gmx editconf -f hetatoms.pdb -o hetatoms.gro
>       *   copy/paste hetatoms.gro into my main .gro file (is there python/utility anywhere for merging .gro files I could leverage?)

Conversion to .gro format is unnecessary; GROMACS handles PDB and other 
formats, if you prefer.

>       *   for ions gromacs doesn’t already know about (ions.itp), follow the instructions described here: http://www.mdtutorials.com/gmx/complex/02_topology.html

Parametrization servers won't generally deal with monoatomic species. In 
a pairwise additive force field, the charge is already fixed and LJ have 
to be tuned, typically based on free energy of solvation.

> (in other words, I’m puzzled why pdb2gmx is complaining about ions it should already know about from the built-in ions.itp)

pdb2gmx doesn't know anything about ions.itp, that comes in later when 
calling grompp. pdb2gmx only knows about what is defined in the force 
field .rtp file(s).



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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