[gmx-users] ligand force field parameters

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 16 13:35:01 CET 2003

> 3) optimize the charges in your molecule in a similar fashion
> as was done for the remainder of the (Gromacs) FF by fitting
> everything to experimental thermodynamic and structural data
> (this IS the way the Gromos/Gromacs FFs were optimised
> isn't it ?)

More or less. Lots of history and trial and error.

It may turn out that it is easier to extend the OPLS force field,
because they use strict combination rules, whereas GROMOS has
interaction matrices, where most interactions are determined by
combination rules, but the parameter depends on the interaction pair in
some cases. 

For a new molecule in OPLS you can refer to the Jorgensen papers to know
how the charges are developed, (and the torsion parameters). Then you
use VdWaals types similar to other atoms for the atoms in your molecule,
and finally fine-tune the parameters to some experimental observables.

Quite a lot of work indeed but the only serious option. Transferability
of parameters to other molecules, in particular charges, is not what
you'd want it to be.

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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