Re: [AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 12 Sep 2012 06:24:59 -0400

You have sent this email twice and been responded to twice. If you did not
get the original responses (from Scott and myself), please check your mail
settings to make sure that Amber emails make it to your inbox.

Scott originally asked for the input files to try to reproduce your issue.
http://archive.ambermd.org/201209/0116.html

Until this happens, there is no way to help you further.

All the best,
Jason

On Wed, Sep 12, 2012 at 5:19 AM, Emanuele Monza <emanuele.monza.bsc.es>wrote:

> Dear all,
>
> I am trying to run a MD of hemoglobin. After preparing all necessary input
> with Xleap I minimize the sistem with Sander (four different minimizations)
> and everything it is fine. Then I have four stages of equilibration (100 ps
> each). These are ran with CUDA version. The simulation dies giving the
> following error message:
>
> *Hydrogen atom 219 appears to have multiple bonds to atoms 220 and 221
> which is illegal for SHAKEH.
> Exiting due to the presence of inconsistent SHAKEH hydrogen clusters.*
>
> There is a problem: Atom 219 is NOT a hydrogen, is a carbon... So I try to
> run normal Sander (no CUDA acceleration) and everything it is fine!
> I am using Amber 11 and preparing the system with Amber Tools 12.
> Do you have any idea of which could be the problem? Thanks in advance.
>
> Best regards,
> Emanuele
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 12 2012 - 03:30:03 PDT
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