Re: AMBER: AMBER 9 - Force Field Options - Question

From: Adrian Roitberg <>
Date: Thu, 18 Oct 2007 14:56:23 -0400

Sorry if you were confused.

I thought I had made myself clear.
The original question was :

"I would like to know is it fine to
combine the glycamxx with the ff03 (Duan) forcefiled in a system?"

You answered "Simple answer to your first Q is yes. We actually do that

So, I simply wanted to know if you had data showing that this is ok.

Again, I am not saying it would not be, and I am not saying other force
fields would do better or worse, I am simply saying that it makes me
uncomfortable to mix and match charge models. Given your answer, I was
looking forward to data that showed it was ok. If so, it would be MUCH
better for everyone.

Now: do you feel comfortable using the mixed charge models based on
their solvation energies being 'similar' ?

Moreover, if they are similar, why change ?

I am REALLY trying to be constructive in the discussion, please do not
take it any other way. There are many things to learn from discussions
like this.


Yong Duan wrote:
> Hi, Carlos,
> I thought Adrian was questioning the validity of parm94 because his main
> concern was the difference in dielectric environment in which the charges
> were derived and parm94 was derived in "gas-phase" :).
> You are right, to validate this, a set of highly accurate absolute binding
> free energies would be desirable. If this is what you meant, the answer is
> no, we have not done it. However, we have calculated the solvation free
> energies of the two charge sets and found they are indeed quite similar.
> yong
> -----Original Message-----
> From: [] On Behalf Of
> Carlos Simmerling
> Sent: Thursday, October 18, 2007 3:07 AM
> To:
> Subject: Re: AMBER: AMBER 9 - Force Field Options - Question
> Hi Yong,
> I think Adrian was asking if you had published a validation of
> the combination, not saying anything about something being
> gas phase. I'd be interested too, and I admit that I also did not
> read the paper that addresses his question- can you give us the ref?
> as far as I could see it's not in the ff03 paper. This would be really
> helpful for people doing protein/nucleic acid complexes, like I do,
> just to see confirmation that the electrostatics are interchangable.
> thanks!
> carlos
> On 10/17/07, Yong Duan <> wrote:
>> Adrian:
>> You obviously did not read the paper :).
>> Parm94 charges are effectively a set of condensed-phase charges, not
> really
>> gas-phase charges. If you look at the dipoles, ff03 and parm94 dipoles are
>> quite simular. The ff03-approach is preferred because it gives a
> systematic
>> way to represent the solvent polarization effect.
>> yong
>> -----Original Message-----
>> From: [] On Behalf
> Of
>> Adrian Roitberg
>> Sent: Wednesday, October 17, 2007 11:27 AM
>> To:
>> Subject: Re: AMBER: AMBER 9 - Force Field Options - Question
>> Yong Duan wrote:
>>> Simple answer to your first Q is yes. We actually do that too. FYI, for
>>> large molecules we often derive charges using parm94 approach. For small
>>> molecules and amino acids, we prefer DFT/cc-pvtz(pcm=ether) charges.
>> Yong,
>> quick question, what do you mean by 'we prefer' ? I presume some
>> validation of the procedure must be there, right ?
>> I do not see how charges derived with such different dielectric constant
>> would be compatible, and in fact I can imagine some simple examples
>> where it would fail.
>> Not that I believe all the other techniques out there either, but just
>> wanted to see what your data was to say that this worked. I believe that
>> the community would benefit from seeing this work if you have not yet
>> published it.
>> Thanks !
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                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
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Received on Sun Oct 21 2007 - 06:07:32 PDT
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