Send me the input files? I'm betting you have some some of invalid SHAKEH
network that the CPU code does not correctly detect.
On Thu, Sep 6, 2012 at 2:08 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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Received on Thu Sep 06 2012 - 09:30:04 PDT
