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