On Tue, Feb 14, 2012, Dilraj LAMA wrote:
>
> If we calculate the net charge of the molecule it is -0.00199 which
> is close to zero. My question is if I now generate the charges of a
> new molecule and get the net charge to be close to the above value,
> can I consider the net charge to be zero for all practical purposes?
Yes.
>
> Secondly, the charge distribution on the hydrogen atoms H121/H122 and
> H111/H112 which is bonded to the carbon atoms C12 and C11 respectively
> are not identical. I was of the understanding that the charge
> distribution on these atoms have to be equal. Is this appropriate?
The current release does not symmetrize charges in the best way. People have
different opinions about how serious an error this is. If you have the time
to tweak things by hand, or to run R.E.D., that might give you better charges.
If you are running a virtual screening of thousands of ligands, that is a less
attractive option.
The equivalence problem should be fixed in the upcoming release.
....dac
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Received on Tue Feb 14 2012 - 05:00:03 PST
