[gmx-users] prodrg and charge groups

[Diane Fournier]

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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