Hi Karl,
Thank you very much for your advises. I will start from soemthing and see how I will end
up.
cheers..
NP
---------------------------------------
Necmettin Pirinccioglu
Department of Chemistry
University of Dicle
e-mail. pirincn at dicle dot edu dot tr
phone. +90 (0412) 2488550 (ext. 3055)
----------------------------------------------
> -----Original Message-----
> From: "Karl N. Kirschner" <kkirsch.scai.fraunhofer.de>
> To: AMBER Mailing List <amber.ambermd.org>
> Date: 09-04-2010 13:12
> Subject: Re: Re[2]: [AMBER] developing amber force field
>
> Hi Necmettin,
>
> A detailed explanation of what you are asking for is very difficult to do in an email.
In my opinion, learning about force field development and then executing that knowledge
requires some training. There are different philosophies towards how it is approached -
for example, as your question points out, how one uses experimental data and quantum data.
Another issue is if you want the force field to be transferable or not.
>
> Here is a a short, undetailed procedure that I use:
>
> 1) Identify the parameters and atom types you want to optimize
>
> 2) Determine the molecules that will be used for optimizing those parameters
>
> 3) Perform restrained quantum optimization on those molecules
> a) restrain the degree of freedom that corresponds to the particular parameter of
interest
> b) perform these restraint optimization at various values of this degree of freedom
(e.g. every 30 degrees for a specific dihedral)
>
> 4) Determine the partial atomic charges for the molecules
>
> 5) Iteratively perform restrained molecular mechanics optimization, adjusting the
parameters until you have them optimized
> a) this restraint corresponds to those used in 3)
>
> 6) Validate the optimized parameter set by comparison experimental data (gas-phase and
solution-phase data)
>
> Now how this is done is difficult to describe in detail and will differ, to some degree,
between different researchers. As mentioned before, it is best to read some force field
papers written by groups who do this (e.g., MM3, Charmm, Parm94, Glycam06, MMFF, OPLS,
Gromos).
>
> Hope that helps some.
>
> Cheers,
> Karl
>
> ----- Original Message -----
> From: "Necmettin Pirinccioglu" <pirincn.dicle.edu.tr>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Friday, April 9, 2010 11:03:51 AM
> Subject: Re[2]: [AMBER] developing amber force field
>
>
> Thank you very much for your reply. Well I have got the papers by Cornell and Wang but I
> need something more basic with explainations about driving bond, angle and dihedral
etc.,
> parameters from qm calculations and x-ray data.
>
> Cheers,
> NP
> ---------------------------------------
> Necmettin Pirinccioglu
> Department of Chemistry
> University of Dicle
> e-mail. pirincn at dicle dot edu dot tr
> phone. +90 (0412) 2488550 (ext. 3055)
> ----------------------------------------------
>
>
> > -----Original Message-----
> > From: InSuk Joung <i.joung.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Date: 09-04-2010 04:44
> > Subject: Re: [AMBER] developing amber force field
> >
> > I am not sure how basic stuffs you want. But, in order to understand AMBER
> > force field, it is a good start to read the paper about FF94 (Cornell et al.
> > JACS 117, 5179). For small molecules, you can search articles with the
> > keyword, GAFF(General AMBER force field). See Wang et al. J comput chem
> > 25,1157.
> > Good luck!
> >
> > On Thu, Apr 8, 2010 at 3:46 PM, Necmettin Pirinccioglu <pirincn.dicle.edu.tr
> > > wrote:
> >
> > > I am interested in developing force field parameters for some small organic
> > > and
> > > organo-metalic compounds. I have searched the literature and internet
> > > including amber
> > > archive but I did not find any basic source regarding how the amber force
> > > fields are
> > > developed from scratch.
> > > I would be glad if you could provide such a source.
> > > Best wishes
> > > Necmettin
> > > ---------------------------------------
> > > Necmettin Pirinccioglu
> > > Professor of Organic Chemistry
> > > Department of Chemistry
> > > University of Dicle
> > > e-mail. pirincn at dicle dot edu dot tr
> > > phone. +90 (0412) 2488550 (ext. 3055)
> > > ----------------------------------------------
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Best,
> > InSuk Joung
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Fri Apr 09 2010 - 04:00:02 PDT
