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
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.
Open Babel has been extended to deal with periodic systems. In that case, please remember to add
periodic_molecules = yesin 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.
Although UFF is in principle a full-periodic-table force-field, there might be cases where:
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:
Further information can be found in the FAQ.
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
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.