Force+fields

=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:

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

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

The script which uses ffld_server and parses its output:

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

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

[|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.

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

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

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

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 * **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.