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
Received on Fri Dec 07 2012 - 04:00:02 PST
