[gmx-users] Re: charges
lindahl at stanford.edu
Tue Oct 22 19:11:35 CEST 2002
Marc Baaden wrote:
>>>>Erik Lindahl said:
> >> CHELPG is stable and good to very good even for large molecules.
>On a more general note, I would not really agree with this depending
>on what you call a large molecule. We used to separate our molecules
>in smaller fragments for charge derivation, as the electrostatic
>potential might be biased towards a particular conformation and give
>more weight to residues on the surface of the molecule if you choose
>too large a fragment. This is of course only relevant if your molecule
>has freely rotatable groups, not if it is very rigid.
>You can also do several conformations of a fragment (eg cis, trans, gauche)
>and check what the effect on the charges is, to see whether you can/
>should average or have to make an informed choice based on the property
>you want to look at.
Sure - in the case I talked about I actually determined the charge for
64 different lipid headgroup conformations and averaged....
And Merz-Kollman might very well be just as good; the main reason for
not using it is that everything else in OPLS/AA is CHELPG.
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