Diane,
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
demanding.
Best wishes,
David Mobley
UCSF
On 6/29/06, Diane Fournier <[EMAIL PROTECTED]> 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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