Yong,
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
too."
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.
Adrian
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: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
> Carlos Simmerling
> Sent: Thursday, October 18, 2007 3:07 AM
> To: amber.scripps.edu
> 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 <duan.ucdavis.edu> 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: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
> Of
>> Adrian Roitberg
>> Sent: Wednesday, October 17, 2007 11:27 AM
>> To: amber.scripps.edu
>> 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 adrian.qtp.ufl.edu
============================================================================
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or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
-- Theodore Roosevelt
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