AMBER Archive (2007)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 18 2007 - 05:06:44 CDT

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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Adrian Roitberg
> Sent: Wednesday, October 17, 2007 11:27 AM
> To: amber_at_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 !
>
> >
> > To your second Q, every ff has some problems if you dig further, given the
> > nature of the ff development. The question is really which one is better.
> > Between parm91 and gaff, my impression is that gaff is a notable
> > improvement.
> >
> >
> > yong
> >
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of
> > WANG,YING
> > Sent: Wednesday, October 17, 2007 8:47 AM
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: AMBER 9 - Force Field Options - Question
> >
> >
> > Hi, Dear all, I also have some question about the forcefield
> > selection and would like to get some help from you..........
> >
> > 1. Now I do simulation of a protein and try to unfold it, I use
> > ff03 (duan) forcefiled. The result is fine until now. Next step I
> > try to bind it with a carbonhydrate and then do simulation of this
> > glyco-protein. I know that I should choose glycamxx forcefiled to
> > deal with the sugar part, but I would like to know is it fine to
> > combine the glycamxx with the ff03 (Duan) forcefiled in a system?
> > Sorry for this stupid question........
> >
> > 2. I also try to do simulation of a linear poly carboxylic acid,
> > could you tell me which force filed I can use? I saw the parm91 is
> > for general organic molecules. Is it too old? The gaff is new but
> > I saw the comments said that it might have problem to deal with
> > some molecules. So I'm confused.............
> >
> > Could anybody give me some suggestion? Or some reference
> > literature? It will be greatly appreciated............
> >
> > Have a good day!
> >
> > Ying
> >
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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_at_qtp.ufl.edu
> ============================================================================
>
> To announce that there must be no criticism of the president,
> 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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-- 
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Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
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Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
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