OK, I see what's going on. In C, numbering begins with 0. In FORTRAN it
begins with 1. If add 1 to each number spouted by the C code, you will
find you have a hydrogen attached to both a carbon and an oxygen.
Sander does not catch this error. It should...
Jason, did you guys fix the FORTRAN in pmemd to detect this yet?
Scott
On Wed, Sep 12, 2012 at 2:19 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 12 2012 - 07:30:03 PDT
