Have you contacted Scott? He sent this response to your original email:
http://archive.ambermd.org/201209/0116.html
On Fri, Sep 7, 2012 at 9:02 AM, Emanuele Monza <emanuele.monza.bsc.es>wrote:
> Hello,
>
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Sep 07 2012 - 08:00:02 PDT
