Hi Giulia,
You can check whether you have the directory under your $AMBERHOME directory:
$AMBERHOME/dat/mtkpp/ZAFF/201108/
In which you can find ZAFF.prep and ZAFF.frcmod. Please treat these two as right ones since the ZAFF.xml file under $AMBERHOME/dat/mtkpp/ZAFF/ directory has some errors in it.
To keep consistent with the prep file, for you pdb file, you need to rename the three Cys residues in the coordination sphere as CY2, one His residue as HE1 and the Zinc ion as ZN2.
Hope it helps,
Pengfei
On Sep 24, 2014, at 3:49 AM, Fonti Giulia <giulia.fonti.epfl.ch> wrote:
> Hello!
>
> I'm having problems with the parametrization of a Zn coordinated by 3 Cys and 1 His epsilon. After running T leap i had a residue charge of 0.76... I used Zaff. xml and Zaff.bcl to obtain the parameters , but i noticed that the total charge is not -1 (3 Cys +His+Zn) but 0.77. Could anyone tell me how to solve this problem for my system and where i could find the right parameters for the Zn ( i used Cy2, He1, Zn2 ).
>
> Thank you so much
>
> Giulia
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Received on Wed Sep 24 2014 - 13:00:03 PDT
