I have now the same issue with small molecule ligand docked into zinc containing atom.
TER record are ok and PDB was not generated by tleap.
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 524773
| TOTAL SIZE OF NONBOND LIST = 3783691
partition error in shake on processor 0
this processor has atoms 1 through 3310
atom 3310 is within this range
atom 3311 is not within this range !
ATOM 3310 C6 RES 211 12.953 -7.656 8.135 1.00 0.00
ATOM 3311 H5 RES 211 12.695 -7.553 9.185 1.00 0.00
ATOM 3312 C4 RES 211 13.722 -8.746 7.726 1.00 0.00
Answers in mailing list were not helpful until so far as this is not water and TER records look ok and file was not from tleap. Maybe file of ligand used for antechamber with all hydrogens was, I ll check that if that can be relevant.
Best regards,
Andrew
02.11.2011, 09:36, "Jason Swails" <jason.swails.gmail.com>:
> 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). šRoss 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. šObviously 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:
>
>> šOn Tue, Nov 01, 2011, Breuer, Marian wrote:
>>>> šI'm currently trying to carry out MD simulations with sander (MPI
>>>> šparallel version, AMBER11) on a protein system using SHAKE bond
>>>> šconstraints for bonds containing hydrogen (sander option ntc=2). These
>>>> šwork with up to 14 processors, but with any number of cores higher than
>>>> šthat the simulations abort in the first step with the error message:
>>>>
>>>> ššpartition error in shake on processor ššššššššššš0
>>>> ššthis processor has atoms ššššššššššš1 šthrough šššššššš8265
>>>> ššatom šššššššš8265 is within this range
>>>> ššatom šššššššš8266 is not within this range !
>> šOK: your prmtop file has bad information in it, so the "problem" is not
>> šwith
>> šsander, but with how the prmtop file itself was generated.
>>
>> šSpecifically, the ATOMS_PER_MOLECULE field in the prmtop has this:
>>
>> š%FLAG ATOMS_PER_MOLECULE
>> š%FORMAT(10I8)
>> šššš8265 šššš848 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1
>>
>> š...etc., which is the reason that sander thinks that atoms 8265 and 8266
>> šare
>> šin different molecules (and hence can be assigned to different processors).
>>
>> šYou seem to have a system with 1 "HER" group, 9 heme groups, a protein,
>> šand a pile of sodiums, chlorides and water. šIt looks like at some point,
>> šthe HER and HEM residues had their coordinates after the regular protein
>> šcoordinates, but that at some point, these HER/HEM atoms got placed before
>> šthe protein ones. šAlso, most likely, each HEM group should be its own
>> šmolecule (which is later cross=linked to the protein somehow. šThis means
>> šthat in the input pdb file, there should have been a TER after the protein
>> šatoms and after each HEM/HER residue. šThen (once all hydrogens are added)
>> šthe first 8265 atoms would be protein (amino acid atoms); there should
>> šthen be 10 HER/HEM residues. šThe ions and water would then be added by
>> šLEaP.
>>
>> šMy wild guess is that either your input pdb file didn't have TER cards in
>> šall
>> šthe required places, or that you used the savePdb command at some point,
>> šthen
>> šre-read that back into LEaP(?) It may well be a bug in LEaP and not
>> šoperator
>> šerror, but I can't tell.
>>
>> šBut this is about as far as I can go...if seeing this description of the
>> šproblem doesn't help, we would need to know the exact commands you used to
>> šcreate the prmtop file.
>>
>> š...good luck...dac
>>
>> š_______________________________________________
>> šAMBER mailing list
>> šAMBER.ambermd.org
>> šhttp://lists.ambermd.org/mailman/listinfo/amber
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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 Sat Nov 26 2011 - 01:00:03 PST
