Force fields


See also:
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

There are several ways to get the topology + force field for an
arbitrary molecule:

  • "Maestro + Desmond" programs of the Schrodinger software pack can
assign OPLS-AA force filed. The parameters are stored in the *.cms file.

  • "FFLD_SERVER" of the Schrodinger software:
$SCHRODINGER/utilities/ffld_server. Also OPLS-AA force filed.

The script which uses ffld_server and parses its output:


You will need to write a script which converts the output to
Gromacs format.

  • "antechamber" + "tleap" of the AmberTools utilities. It can assign
any kind of Amber force field, like General Amber Force Field.
See an example:

http://compchemmpi.wikispaces.com/Scripts#GenAmberTop
You could use the "amb2gmx" script to convert the generated Amber
topology to Gromacs format:
http://ffamber.cnsm.csulb.edu/ffamber-tools.html

  • ''PRODRG server'' for the united atom GMX force fields.

  • ''Vega ZZ'' and "Vega" can assign OPLS-AA force field, but not all
atom types, bonds etc. are supported.

  • "MCCCS Towhee'' monte carlo code can assign very many force
fields, but, first, one has to create the so-called basic connectivity
map (which atom is covalently bound to which).
//towhee.sourceforge.net/

  • Automated topology builder for GROMOS like force fields;
http://compbio.biosci.uq.edu.au/atb/

  • SwissParam: This service provides topology and parameters for small organic molecules compatible with the MERK MOLECULAR FF all atoms force field, for use with CHARMM and GROMACS.
http://swissparam.ch/