Hi Outi,
I'd recommend consulting the following paper where the procedure to develop
amber FF for metal sites is presented:
J. Chem. Theory Comput. 2010, 6, 2935-2947
all the best,
Tomasz
2012/12/7 francesco oteri <francesco.oteri.gmail.com>
> Hi Outi,
>
> 2012/12/7 <osalo.abo.fi>
>
> > Dear AMBER specialists,
> >
> > I am following the AMBER tutorial A1 (old and new) and trying to
> > figure out how I need to develop the parameters for my
> > histidine that is bound to copper(II).
> >
> > I am first trying to run Gaussian geometry optimization for the HID-CU
> > complex. I assume my copper has a charge +2 and it is penta-coordinated
> at
> > the
> > binding site...with two HIDs, one HIE and two water molecules....
> >
> > How do I define the multiplicity for the HID-CU complex? How many
> > unpaired electrons are there?
> >
>
> > Or should I calculate the whole complex with HIE, 2 HIDs and 2 water
> > molecules as well?
> >
> > A good clue regarding unpaired electrons are EPR experiments, if you have
> such a data
> (or if you can find them), it is a good starting point.
>
>
>
> > Or is it better to do it separately for HID-CU and HIE-CU and then try
> > to do the charge fitting (RESP) for these and then create the library
> > files for HID-CU and HIE-CU (without CU for all others but one
> > histidine?). How can I get the missing force field parameters with
> > Gaussian? What kind of calculation I should run?
> >
>
> In my opinion it is better using as much as you can, so if you can optimize
> the whole complex it is better.
> Regarding the HID and HIE you can just consider the sidechains and a methyl
> group instea of the C-betha
> (whose charges I advice to constrain to the same value the charges of the
> C-betha + hydrogens have in the force
> field you are going to use).
> Treating the water molecules is quite tricky 'cause they move, so I suggest
> to constrain their charges
> to the value of the standard model you are planning to use.
>
>
> >
> > And finally, if I follow your tutorials, should I then use the ff99SB
> > forcefield in my MD calculations or can I use ff03.r1?
> >
> >
> This is up to you, of couse :) Consider there other AMBER force-fields that
> could perform better!
>
>
> > Thanks a lot for your advice!
> >
> > Outi
> >
> >
>
> Francesco
>
>
>
> > --
> > Dr. Outi Salo-Ahen
> > Åbo Akademi University
> > Department of Biosciences, Biochemistry
> > Tykistökatu 6 A
> > FIN-20520 Turku
> > E-mail: outi.salo-ahen.abo.fi
> > Tel: +358-2-215 4009
> > Fax: +358-2-230 5018
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Tomasz Borowski, PhD, D.Sc.
Jerzy Haber Institute of Catalysis and Surface Chemistry
Polish Academy of Sciences
ul. Niezapominajek 8
30-239 Krakow, Poland
phone: +48 12 6395158
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 08 2012 - 22:30:02 PST
