Also, add a line in your leap file as the following:
addAtomTypes { { "ZN" "Zn" "sp3" } { "S4" "S" "sp3" } { "N3" "N" "sp3" } }
*Best,*
*Satyajit Khatua,*
*Post-doctoral fellow,*
*Department of Chemistry,*
*Georgia State University,*
*Atlanta, GA **30302.*
On Mon, Sep 16, 2024 at 3:17 PM SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
wrote:
> 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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>>
>
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Received on Mon Sep 16 2024 - 12:30:04 PDT
