Re: AMBER: how to reassign charges

From: David Mobley <>
Date: Wed, 9 Aug 2006 13:03:10 -0700


I am not too sure exactly what your problem is, as if I add up the
charges for toluene listed on the tutorial page, the net charge is 0,
meaning that it's already neutral. Are you using different charges you
got from somewhere? Or are you just trying to repeat the same
procedure for ff03? If that's the case, the basic idea is that you
just want toluene to end up neutral at the end, and it's not clear to
me that there is any one "right" way to do this.

In other words, I think your question isn't particularly well-defined.
You're asking what the "right" way to make toluene neutral is when you
create toluene by deleting atoms from PHE, which is neutral. To some
extent, partial charges will be different in toluene then in PHE, so
it's not clear to me that there is a "right" way to modify the charges
to get neutrality -- the charges will redistribute around toluene
according to the underlying chemistry, and you can either make a guess
at this, or you can just arbitrarily adjust the charge in certain
places (as for the tutorial), or...

On the other hand, you COULD say that the "right" way will be the way
that gives you the charges that are appropriate for toluene (not PHE)
in water. If you want to know the "correct" charges for toluene, I
suppose you could create a mol2 file of toluene and run it through
antechamber to use the am1-bcc method to calculate charges for

Still, it's all a bit of a moot point, in my opinion... If you're just
trying to make sure you can repeat the free energy calculation shown
in the tutorial, you've apparently already done that, so I'm not sure
why you're still concerned about it.


On 8/9/06, Lwin, ThuZar <> wrote:
> Dr. Case,
> In following the tutorial on Thermodynamic integration, I am able to
> reproduce closely to the data in the tutorial. However, I have question
> regarding with making the toluene system neutral.
> When I compare charges on toluene in tutorial and phenylalanine (in
>, all atoms are the same except CB which is -0.03430 in PHE
> and -0.0828 in toluene. So -0.0485 was added to -0.03430 to make the
> toluene neutral. This 0.0485 happens to be the net charge of toluene after
> removing N, CA,C=0, the atoms we do not want for toluene.
> I tried to do similar approach using ff03, that is I added the net
> charge left on toluene after removing N, CA,C=0 from PHE, to make toluene
> neutral to the CB atom.
> In CB of PHE has charge -0.09872. I changed it to
> -0.183400 since the net charge on toluene was 0.08468. I then redid the
> thermodynamic integration. This time my results are not in agreement with
> the experiment. The charging free energy in vacuum now becomes almost twice
> the value of charging in vacuum as in tutorial, besides it is a positive
> value.
> So my question is how do I appropriately assign the charges on toluene so
> that it would be neutral.
> Thank you,
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Received on Sun Aug 13 2006 - 06:07:03 PDT
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