[gmx-users] Generating a .gro file from .pdb file

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Sep 28 20:01:29 CEST 2009


> No, that procedure generates a topology file, it is not the correct tool for
> a change of coordinate format (which is almost never needed anyway). As a
> side effect, it regularizes an input coordinate file which might have been
> in one of various formats, and outputs a coordinate file whose default
> format happens to be .gro (but could be a range of possibilities). I wish
> tutorial writers would not give new people the wrong impression about the
> purpose of this step!

>From my tutorial (http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html):

Structure conversion and topology

A molecule is defined by the coordinates of the atoms as well as by a
description of the bonded and nonbonded interactions. Since the
structure obtained from the PDB only contains coordinates, we first
have to construct the topology, which describes the system in terms of
atom types, charges, bonds, etc. This topology is specific to a
certain force field and the force field to be used is one of the
issues requiring careful consideration. Here we use the GROMOS96 53a6
united atom force field, which is parameterized to give good
predictions of free energies of solvation of amino acid side chains
and which generally gives good agreement with NMR experiments.
It is important that the topology matches with the structure, which
means that the structure needs to be converted too, to adhere to the
force field used. To convert the structure and construct the topology,
the program pdb2gmx can be used. This program is designed to build
topologies for molecules consisting of distinct building blocks, such
as amino acids. It uses a library of building blocks for the
conversion and will fail to recognize molecules or residues not
present in the library. Issue the following command to convert the
structure; choose the GROMOS 53a6 force field when prompted. Note the
flag -ignh, which causes hydrogen atoms present in the file to be
removed, and to be rebuild according to the description in the force

pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh

Read through the output on the screen and check the choices made for
the histidine protonation and the resulting total charge of the
protein. Also browse through the input structure file (protein.pdb,
pdb format) and output structure file (protein.gro, gromacs format).
Note the differences between the two formats. Also note that the
output structure file could as well have been chosen to be in pdb
format. Now browse through the topology file and look at the

Write down the number of atoms before and after the conversion and
explain the difference

List the atoms, atom types and charges from a tyrosine residue as
given in the topology file



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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