[gmx-users] charges

Yiannis Nicolis ioannis.nicolis at free.fr
Wed Apr 14 02:36:01 CEST 2004

I used prodrg charges but now I simulate with oplsaa and prodrg does 
not produce opls topologies. If you use gmx force field prodrg seems a 
good option.
For opls, if all my atoms types are in the ffoplsaa.atp and I don't 
have deprotonation I use the charges of ffoplsaanb.itp file.
If not, I tried the PETRA server 
<http://www2.chemie.uni-erlangen.de/services/petra/> or QM from Mopac 
or Gamess. And as for QM there are various possibilities, you end up 
with a few sets of charges to test.
As you said, I am not sure there is a clear answer. Some (sorry, I 
don't remember if that's a paper, a book or this mailing list) suggest 
to scale the QM charges with a factor taking into account polarization 
in the solvent. With neutral molecules a 1.3 factor one or two times 
gave me "similar" charges with those of the  ffoplsaanb.itp file, but 
it's far from a general rule. And if I try to scale the charges of a 
charged molecule without modifying the net charge (by differently 
scaling positive and negative charges) the result is aberrant. The 
ideal would be to have experimental dipole moment values and try to 
scale the QM partial charge distribution in order to reproduce the 
dipole moments.

Le 13 avr. 04, à 23:54, Coincon Mathieu a écrit :

> Hi,
> I know that this topic is generously covered by the FAQ archives but it
> looks like everyone has his own answer.
> So what's the best way to determine partial charges for a new topology 
> ?
> QM?
> homology with groups in ff*.rtp?
> Fortune telling?
> Ps:Many thanks to David Van der Spoel for your last answer.
> --
> Mathieu Coincon PhD Student
> Universite De Montreal/Departement de biochimie
> Pavillon Roger Gaudry Local D345
> (514).343.6111 #5352
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list