[gmx-users] PRODRG and partial charges

Anton Feenstra feenstra at chem.vu.nl
Mon Aug 18 10:05:01 CEST 2003

Douglas Ridgway wrote:
> I'm confused about how to assign partial charges. I did some browsing of 
> the archives, so I know this has come up before, and have started to read 
> some papers, but I'm still confused.
> Do charges need to be parameterized with the rest of a force field?  Will
> they depend on cutoffs, other molecules and such? How do you do this for a
> new molecule? How arbitrary is it? And how do you figure out what results
> to believe?

For a 'quick-and-dirty' guess at charges, I simply look at 'similar' groups
in the existing forcefield. Also, I've been using Gasteiger charges.
These are trivial to get, and come out at the same range as charges of
comparable groups are in the Gromos forcefields.

To answer the rest, yes, charges are an integrated part with all the rest
of the forcefield and can only be parametrized accordingly. They are not
transferable between forcefields. Phylosophies for assigning charges differ
between the (major) forcefields. (This also means LJ parameters are not
transferable, since the combination determines the interaction between
atoms.) In Amber, they are taken from the prescribed 'Resp' procedure.
In Gromos/Gromacs, they are simply another set of adjustable parameters.

You should parametrize on things like liquid density, heat of vaporization,
and partitioning properties. (Which, if done properly, is a lot of work.)


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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