Hi Karl,
I'm interested in developing a non-transferable forcefield for a small
inorganic molecule (12 atoms). My doubt is about the process of fitting the
parameters to the QM data. Once I'm done with the restrained QM
optimizations, and I have, for example, a potential energy profile for a
certain dihedral angle, what procedure can I use to fit the parameters of a
Furier series to the dihedral's QM potential energy profile? Is it a
try-and-error procedure or is there some systematical method available?
I don't expect a detailed explanation, which I'm sure would be quite
extence. But I would really appreciate it, if you could give me some time
saving directions on the subject.
Thank you very much in advance.
Diego Alonso de Armiño.
Tucumán, Argentina.
2010/4/9 Necmettin Pirinccioglu <pirincn.dicle.edu.tr>
>
> 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)
> > > > ----------------------------------------------
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Best,
> > > InSuk Joung
> > > _______________________________________________
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> >
> >
> >
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>
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Received on Fri Apr 09 2010 - 10:00:06 PDT
