On Tue, Nov 01, 2011, Breuer, Marian wrote:
>
> >
> > I'm currently trying to carry out MD simulations with sander (MPI
> > parallel version, AMBER11) on a protein system using SHAKE bond
> > constraints for bonds containing hydrogen (sander option ntc=2). These
> > work with up to 14 processors, but with any number of cores higher than
> > that the simulations abort in the first step with the error message:
> >
> > partition error in shake on processor 0
> > this processor has atoms 1 through 8265
> > atom 8265 is within this range
> > atom 8266 is not within this range !
OK: your prmtop file has bad information in it, so the "problem" is not with
sander, but with how the prmtop file itself was generated.
Specifically, the ATOMS_PER_MOLECULE field in the prmtop has this:
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
8265 848 1 1 1 1 1 1 1
...etc., which is the reason that sander thinks that atoms 8265 and 8266 are
in different molecules (and hence can be assigned to different processors).
You seem to have a system with 1 "HER" group, 9 heme groups, a protein,
and a pile of sodiums, chlorides and water. It looks like at some point,
the HER and HEM residues had their coordinates after the regular protein
coordinates, but that at some point, these HER/HEM atoms got placed before
the protein ones. Also, most likely, each HEM group should be its own
molecule (which is later cross=linked to the protein somehow. This means
that in the input pdb file, there should have been a TER after the protein
atoms and after each HEM/HER residue. Then (once all hydrogens are added)
the first 8265 atoms would be protein (amino acid atoms); there should
then be 10 HER/HEM residues. The ions and water would then be added by
LEaP.
My wild guess is that either your input pdb file didn't have TER cards in all
the required places, or that you used the savePdb command at some point, then
re-read that back into LEaP(?) It may well be a bug in LEaP and not operator
error, but I can't tell.
But this is about as far as I can go...if seeing this description of the
problem doesn't help, we would need to know the exact commands you used to
create the prmtop file.
...good luck...dac
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Received on Tue Nov 01 2011 - 19:00:02 PDT
