AMBER Archive (2007)

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

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Oct 17 2007 - 13:26:56 CDT

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
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