Dear all,
Thank you so much for this information. I used indeed an input pdb that I had written out from xleap before; but I checked it and it did contain all necessary TER specifiers. The hemes (incl. "HER") had already been at the beginning above the protein atoms in the original pdb, and the number of protein atoms written out by xleap (8365) is not even equal to the actual number of protein atoms (8363; maybe xleap somehow counted two TER lines in between the protein atom lines that terminate two subchains of my protein). I thus would give parmed a try.
.Jason: Can you tell me where to get parmed? I couldn't find it in the latest AmberTools version available on ambermd.org (nor anywhere else on the website). I'd also need the documentation on this tool (I couldn't find it in the AmberTools documentation).
Thanks and best wishes,
Marian
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 02 November 2011 05:36
To: AMBER Mailing List
Subject: Re: [AMBER] Issue with running sander with SHAKE
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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 04 2011 - 10:30:04 PDT
