Discussion group for the ARIA software

["Kelly, Mark" <Mark.Kelly AT ucsf.edu>]

Hello David/Aria-Discuss,

thanks for the tips with a shorter time-step (0.001) we have been able to calculate structures with the Cys4-Zn centre.

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?

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
    -----------------------------------------------------