Re: partial charges for organic ligands

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Sat Mar 26 2011 - 22:18:50 CDT

You can use swissparam.ch for topologies and parameters for ligands, provided
your molecules are in mol2 format.

Richard

________________________________
From: Francesco Pietra <chiendarret_at_gmail.com>
To: Branko <bdrakuli_at_chem.bg.ac.rs>
Cc: NAMD <namd-l_at_ks.uiuc.edu>
Sent: Sat, March 26, 2011 3:23:05 PM
Subject: Re: namd-l: partial charges for organic ligands

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 (i.e.no 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

thanks
francesco

On Sat, Mar 26, 2011 at 6:42 PM, Branko <bdrakuli_at_chem.bg.ac.rs> 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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