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Re: [aria-discuss] CCPN/Aria2.3.1 Two Zn Centers/Fingers Structure Calculation


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  • From: David Langelaan <dlangela AT dal.ca>
  • 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
  • Date: Fri, 28 Feb 2020 12:18:07 +0000
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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:
http://aria.pasteur.fr/archives/aria2.3.2.tar.gz

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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