I've seen tleap do very weird things determining the ATOMS_PER_MOLECULE and
SOLVENT_POINTERS section of the topology file, so I KNOW there's a bug
there for some corner cases (that are becoming more common). Ross can
attest to this as well -- it has caused weird segfaults in pmemd and sander
with strange systems that we've both looked into.
That's why I added a function in my prmtop editor (parmed) to reset this
section completely based on the actual bonded atom network. Obviously not
as ideal as fixing it in leap itself, but it's a quick way of testing
whether or not this will fix the issue...
(The parmed command is "setMolecules solute_ions=True" if you were
interested in trying this to see if it fixes the issue)
All the best,
Jason
On Tue, Nov 1, 2011 at 9:48 PM, case <case.biomaps.rutgers.edu> wrote:
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 01 2011 - 23:00:03 PDT
