AMBER Archive (2006)
Subject: RE: AMBER: how to reassign charges
From: Yong Duan (duan_at_ucdavis.edu)
Date: Wed Aug 09 2006 - 16:26:10 CDT
Dear ThuZar and David:
I don't have much to add on David's comments. Rather, I like to comment on
the charge fitting procedure in general.
In the simplest approach, one can remove a group and use the existing
charges. But more often than not, the interaction with the "removed" group
could have changed the charge distributions. So, an alternative way is to
refit the charges using the methods consistent with the underlying approach
of either ff03 or ff94.
I realize this is rather confusing since the sole purpose is to compare the
force field parameters against experiments and one in fact has to use a
different charge set to do this. To be frank, I am not sure if I can
convince the reviewer that "refitting" would be a reasonable approach.
Nevertheless, it does not sound too great to simply remove a group, although
opinion could differ. The underlying implication of the "removal" approach
is that the charge models are essentially additive that the main chain
charges do not affect the distributions of the side chain charges. I am
unaware of any theory to back up this, though.
On the other hand, I am reasonably glad that your number is only twice as
large. So, it sounds like that the approximation does work to some degree.
> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of David Mobley
> Sent: Wednesday, August 09, 2006 1:03 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: how to reassign charges
> 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 <ThuZar.Lwin_at_stjude.org> 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_amino94.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 all_amino03.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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