Dear Outi,
Copper electronic config.: [Ar].3d10.4s1
Cu(II) -> [Ar].3d9
this means one single electron; i.e. spin multiplicity = 2
(i.e. number of single electron(s) +1)
the total charge of your complex = +2 + (sum of formal negative
charges of the ligands)
pay attention between the HIE, HID and HIP residues for Histidine
HIP (total charge = +1) is unlikely to connect Cu++
let's say the five ligands are: H2O (doublet) HID (doublet), HIE
(doublet), Asp(-1) and Glu(-1); the total charge of your complex will
be +2-1-1 = 0
you could use R.E.D. Server to do this type of job
starting/transforming each ligand/connecting residue into a dipeptide
(ACE-AA*-NME; AA* connecting residue)
See tutorials at q4md-forcefieldtools.org
regards, Francois
> 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?
>
> 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?
>
> And finally, if I follow your tutorials, should I then use the ff99SB
> forcefield in my MD calculations or can I use ff03.r1?
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 12 2012 - 22:30:02 PST
