Hi Debarati,
Going through the coordination environment, you have the type 4 possibility
of ZAFF (look at the table in
https://ambermd.org/tutorials/advanced/tutorial20/ZAFF.php).
So, in your PDB file, rename the CYS as CY4, HIS as HD2 and Zinc ion as
ZN4. I hope this will generate your topology and coordinate, provided the
ZAFF frcmod and prep file correctly sourced.
*Thanking you,*
*Yours sincerely,*
*Satyajit Khatua,*
*Post-doctoral fellow,*
*Department of Chemistry,*
*Georgia State University,*
*Atlanta, GA **30302.*
On Mon, Sep 16, 2024 at 3:02 PM Debarati DasGupta via AMBER <
amber.ambermd.org> wrote:
> Hi experts on the ZAFF research and modeling,
> I am new to modeling proteins with the Zn cation and I am working on
> prepping the system to run a MD on it.
>
> I have two cysteines (named them as CYM) and two histidine's (named as
> HE1) that chelate with the Zn2+ the NE2 chelating with the ZN. { followed
> this suggestion from Pengfei http://archive.ambermd.org/201407/0217.html)
>
> I have pulled in the ZAFF ff and the associated ff19SB the ions and the
> solvent ff. Not sure why I am still unable to get the parameters generated,
> Any ideas on where I should look?
>
> Thanks
>
>
> [cid:794f9367-412a-40ab-a539-9417663b616c]
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Received on Mon Sep 16 2024 - 12:30:03 PDT
