[gmx-users] prodrg and charge groups

David Mobley dmobley at gmail.com
Thu Jun 29 20:34:42 CEST 2006


I can't speak to charge groups, but in terms of charges, I think I
remember that prodrg has a number of disclaimers about its charges.
Personally, I would be rather reluctant to use prodrg charges for
simulating ligands. A fast alternative would be to download the
Antechamber package, which can calculate am1-bcc charges, and run
pdb's/mol2 files for your molecules through it to get charges output
to a mol2 file, then write a little script to take these charges and
use them in your topology instead of those from prodrg.

Although am1-bcc charges are semi-empirical, we've been doing a pretty
extensive test of charge sets (including QM potentials from various
levels of theory fit with RESP) across a large series (well, 40-ish)
of molecules and are finding that am1-bcc charges actually give
hydration free energies that are in the best agreement with experiment
(RMS error about 1 kcal/mol in TIP3P). The best QM calcs roughly
comparable in terms of RMS error, but are obviously substantially more

Best wishes,
David Mobley

On 6/29/06, Diane Fournier <diane.fournier at crchul.ulaval.ca> wrote:
> I don't know if this has already been discussed, but I'm wondering how the
> charges and charge groups are assigned by PRODRG. I'm curious about this
> because I have been using it for a few similar ligands which all contain a
> steroid (estradiol) moiety. In the three cases, the charge groups and
> charges that were assigned were quite different for the estradiol part.
> Also, when compared to the partial charges found for the phenol group of
> tyrosine in the amino acid topologies, the phenol group charges for
> estradiol make no sense (they should be quite similar, right ?). What I've
> been doing until now is to modify the charges and charge groups so that they
> are identical for the estradiol moiety in all cases (so that this part
> displays the same behavior in all simulations). Is this the right way to
> proceed ?
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