Re: partial charges for organic ligands

From: Francesco Pietra (
Date: Sat Mar 26 2011 - 15:23:05 CDT

I could easily calculate ESP or RESP charges, too, with gamess-us. In
that case I could use the multiconformation approach, although most my
ligands should not have any huge dependence of partial charges from
conformation ( possibility of intramolecular annihilation of
charges, and so on). My question was which one of the charge methods
might be most fitting with par_all27_prot_lipid.prm for the protein,
membrane and water, in combination with amber's gaff ff (AM1-BCC, ESP,
RESP, etc) for the organic ligand by using namd. Thus, not a guess,
rather an actual comparison made. If none exists, it is time for me to
do that before going on with uncertain assumptions


On Sat, Mar 26, 2011 at 6:42 PM, Branko <> wrote:
> Gasteiger and OPLS charges are common. If you want something more
> sophisticated charges for ligand and close surroundings only, you can
> calculated it for initial state on semiempirical level (single point
> calculations) by using, for example, PM6 and/or PM6-DH2 that account for
> noncovalent interaction.
> Branko
> On 3/26/2011 5:45 PM, Francesco Pietra wrote:
> Hello:
> Is it any experience with partial charges of different origin for
> non-covalently-bound paired-electrons ligands of proteins (ff charmm
> with namd)? To minimize efforts (since I am not using paratool), I am
> starting with AM1-BCC partial charges for an ensemble in explicit
> membrane-water. The system reaches npt stability nicely. However, I
> wonder whether it is already known that other types of charges for the
> organic molecule may better approximate reality.
> thanks
> francesco pietra
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