Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Hi Mark,

> We also have a 2nd Cys3His-Zn centre. We now tried to add that by first 
> deprotonating the His in the sequence/chain A within CCPN Analysis. We 
> then added the 2nd Zn patch within Aria. Do we need to turn on the His 
> patch within Aria as well?

Yes, You'll have to add the corresponding HIS patch(es), e.g. with SSSD 
Zinc -> HISD patch (means His is HD1 protonated and Zn is bound to His NE2).

Best,

Benjamin

> Best,
>
> Mark
>
>
>
>
>
> ------------------------------------------------------------------------
> *From:* David Langelaan <dlangela AT dal.ca>
> *Sent:* Friday, February 28, 2020 4:18
> *To:* aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>; 
> Kelly, Mark <Mark.Kelly AT ucsf.edu>
> *Subject:* Re: [aria-discuss] CCPN/Aria2.3.1 Two Zn Centers/Fingers 
> Structure Calculation
> Hello Mark,
>
> I have used Aria to calculate structures with three Cys3His-Zn centers 
> and remember running into similar issues with random structures failing. 
> Changing the random seed would work, but then other structures would 
> eventually crash.
>
> In the end I imported the CcpNMR project and  used the zinc patches in 
> the ARIA GUI to build the initial molecule. As for the crashes, from my 
> memory this had to do with the energy minimization somehow becoming 
> unstable. For me a combination of switching from torsion angle to 
> cartesian dynamics and/or shortening the timestep of the calculation 
> solved the problem. The structure calculation ran slower, but at least 
> it ran consistently. I am not sure if your issue is the same, but it may 
> help.
>
> Cheers,
>
> David
>
> On 2020-02-28, 5:09 AM, "aria-discuss-request AT services.cnrs.fr on 
> behalf of Benjamin Bardiaux" <aria-discuss-request AT services.cnrs.fr on 
> behalf of bardiaux AT pasteur.fr> wrote:
>
>      Dear Mark,
>
>      The latest aria version (2.3.2) should automatically add the Zinc ions
>      that you specify in the Zn patches. Or, you could also add each 
> zinc in
>      a separate chain in the CCPN molecular system and select all CCPN 
> chains
>      in ARIA.
>
>      You can add any number of Zn patches as needed in the aria gui. Each
>      zinc must be in a different chain.
>
>      You can download aria2.3.2 here:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__aria.pasteur.fr_archives_aria2.3.2.tar.gz&d=DwIGaQ&c=iORugZls2LlYyCAZRB3XLg&r=298wo5FTw8hoVM2Z8-GREvQZopmfLGcC8YyMqGWWpmw&m=wg14vk5x7Jk7lgjehycxBVV9_FlcA5SL1SCoCqqwpnM&s=1OEpvr8hBs3nBO3W9VcyzzTqvDHRa6jCeR8oEUZqnec&e= 
>
>
>      Best,
>
>      Benjamin
>
>      On 2/27/20 5:06 AM, Kelly, Mark wrote:
>      >
>      > Hello Aria list,
>      >
>      > we are trying to calculate a structure of a protein with two Zn 
> fingers/centers:
>      >
>      > Cys4-Zn
>      >
>      > Cys3His-Zn
>      >
>      > how should we do this in CCPN and Aria2.3.1 if we have two centers?
>      >
>      > Thanks,
>      >
>      > Mark
>      >
>      >
>
>      --
>      -----------------------------------------------------
>      Dr Benjamin Bardiaux    | Bioinformatique Structurale
>      bardiaux AT pasteur.fr     | Institut Pasteur
>      25,28 rue du Docteur Roux 75015 Paris, France
>      -----------------------------------------------------


--
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Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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