OBGMX (β-release)

GROMACS topology generator using Open Babel.

NEWS
August 6, 2015: Updated with a new version, based on OpenBabel 2.3.2.
Notice that this version will give different topologies with respect to the previous one, due to some bugfixes in the UFF implementation of OpenBabel.

Welcome to the OBGMX server,

OBGMX is a tool for generating molecular topologies for the GROMACS simulation package. The current version implements the Universal Force Field (UFF), slightly adapted to the functional forms for the bonded interactions that are available within GROMACS.
The assignment of UFF atom types and the calculation of the molecular connectivity (identifying bonds, angular, torsional and inversion terms) is performed using the routines available in the Open Babel package.

Open Babel has been extended to deal with periodic systems. In that case, please remember to add

periodic_molecules = yes
in your GROMACS' .mdp input file.

Notice that the functional forms for the bonded interactions available in GROMACS do not match the ones required by UFF.
We approximated them in the best way possible. Please check the OBGMX paper for details.

Although UFF is in principle a full-periodic-table force-field, there might be cases where:

  1. UFF does not offer a suitable parametrization of an element in a particular chemical environment;
  2. OBGMX fails in assigning the correct atom type.
To help coping with these situations, we give the possibility to set the geometrical parameters of the topology from the provided configurations.
By checking the proper boxes in the input form on the right, the equilibrium values for the bond lengths, the angles or the dihedrals (at the user's option) can be taken from the provided geometry.
In this case, the energy parameters appearing in the bonded interaction formulae will be still obtained from UFF.

There are to more user-selectable options:

  • Combination rules: UFF suggests to use geometric combination rules for both the ε and σ Lennard-Jones parameters, and this is the default. Users can decide to use the Lorentz-Berthelot combination rules instead (that is: arithmetic average for σ and geometric average for ε)
  • Form of the angular potential: the GROMACS' angular potential closest to UFF's is the G96 angular potential, and this is chosen as the default. However, an harmonic form can also be selected.

Further information can be found in the FAQ.


Please acknowledge OBGMX

If you use OBGMX satisfactorily in you research, please consider citing some of the papers that we have published using it, as well as the GROMACS papers and the Open Babel paper.

The suggested citation is:

G. Garberoglio. OBGMX: a web-based generator of GROMACS topologies for molecular and periodic systems using the Universal Force Field. J. Comput. Chem. 33 (2012), 2204-2208
doi: 10.1002/jcc.23049
http://software-lisc.fbk.eu/obgmx/

Access OBGMX

Please select the coordinate file to upload:

In principle, any format that can be processed by Open Babel (release 2.3.1) is acceptable. OBGMX is usually tested with xyz files for molecular systems or pdb files for periodic systems.
Please notice that during the β-testing phase, the topology generation is limited to systems smaller than 1000 atoms.

Type of combination rules:

Weight for the 1-4 interaction (between 0.0 and 1.0):

Type of angular potential form:

Use equilibrium bond lengths from the input file
Use equilibrium angles from the input file
Use equilibrium dihedrals from the input file

PLEASE NOTICE that the file that you upload will be saved on our servers. We cannot offer any guarantee of confidentiality or non-disclosure.
If you cannot abide by these terms, do not submit any structure.

After pressing the Submit button, you will be redirected to a page with your topologies.
Please check here for an explanation of what will be obtained.


OBGMX is currently in beta release. This roughly means that it suits the purposes of its creator.
Please check carefully the output, because we cannot offer any guarantee that UFF has been implemented correctly (although we tried to do our best).

If you want to report problems either with this web site, or with the generated topologies, you are welcome to drop a line to garberoglio [AT] fbk [DOT] eu
Your feedback will be appreciated, but please notice that our resources are currently quite limited, and we might not be able to reply to everyone.

OBMGX was developed by Giovanni Garberoglio.
Interdisciplinary Laboratory for Computational Science (LISC)
Fondazione Bruno Kessler and University of Trento, Italy.