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?
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?
Thanks a lot for your advice!
Outi
--
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
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Received on Fri Dec 07 2012 - 00:30:01 PST
