Just checked parametrization again.
After saveamberparm I did savepdb everything was ok. When I convert prmtop and inpcrd back to PDB I get the residues mess problem. So there is apparently some problem with parametrization.
Best regards,
Andrew
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26.11.2011, 21:45, "Andrew Voronkov" <drugdesign.yandex.ru>:
I have found indication of problem, but have no idea how to solve it.
In PDB file created from inpcrd and prmtop there is one RES atom from ligand in protein:
ATOM šš3308 šO ššGLU šš210 ššššš58.563 š30.137 š20.807 š1.00 š0.00 ššššššššššO
ATOM šš3309 šOXT GLU šš210 ššššš59.202 š29.891 š18.732 š1.00 š0.00 ššššššššššO
ATOM šš3310 šC6 šRES šš211 ššššš47.114 š26.505 š42.295 š1.00 š0.00 ššššššššššC
TER
ATOM šš3311 šH5 šRES šš211 ššššš46.856 š26.607 š43.346 š1.00 š0.00 ššššššššššH
ATOM šš3312 šC4 šRES šš211 ššššš47.882 š25.415 š41.887 š1.00 š0.00 ššššššššššC
ATOM šš3313 šH3 šRES šš211 ššššš48.209 š24.689 š42.629 š1.00 š0.00 ššššššššššH
but this was not the case in original PDB, so I have no idea why it has migrated.
What might be the reason for this?
The initial PDB file was this:
ATOM šš1685 šC ššGLU šš210 ššššš23.190 š20.522 šš4.241 š1.00 š0.00 ššššššššššC
ATOM šš1686 šO ššGLU šš210 ššššš23.659 š21.648 šš3.992 š1.00 š0.00 ššššššššššO
ATOM šš1687 šOXT GLU šš210 ššššš23.806 š19.469 šš3.926 š1.00 š0.00 ššššššššššO
TER ššš1688 šššššGLU šš210
HETATM 1689 šC1 šRES šš211 ššššš23.181 š41.843 š13.592 š1.00 š0.00 ššššššššššC
HETATM 1690 šC2 šRES šš211 ššššš14.795 š45.766 š16.068 š1.00 š0.00 ššššššššššC
HETATM 1691 šC3 šRES šš211 ššššš15.158 š46.148 š17.360 š1.00 š0.00 ššššššššššC
HETATM 1692 šC4 šRES šš211 ššššš22.058 š43.937 š13.012 š1.00 š0.00 ššššššššššC
HETATM 1693 šC5 šRES šš211 ššššš21.049 š41.831 š12.394 š1.00 š0.00 ššššššššššC
HETATM 1694 šC6 šRES šš211 ššššš20.991 š44.620 š12.429 š1.00 š0.00 ššššššššššC
so there it was not separated.
Best regards,
Andrew
26.11.2011, 12:38, "Andrew Voronkov" <drugdesign.yandex.ru>:
> šI have now the same issue with small molecule ligand docked into zinc containing atom.
> šTER record are šok and PDB was not generated by tleap.
>
> šAPPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> ššusing šš5000.0 points per unit in tabled values
> ššTESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> š| CHECK switch(x): max rel err = šš0.2738E-14 ššat šš2.422500
> š| CHECK d/dx switch(x): max rel err = šš0.8314E-11 ššat šš2.736960
> šš---------------------------------------------------
> š| Local SIZE OF NONBOND LIST = šššš524773
> š| TOTAL SIZE OF NONBOND LIST = ššš3783691
> ššpartition error in shake on processor ššššššššššš0
> ššthis processor has atoms ššššššššššš1 šthrough šššššššš3310
> ššatom šššššššš3310 is within this range
> ššatom šššššššš3311 is not within this range !
>
> šATOM šš3310 šC6 šRES šš211 ššššš12.953 š-7.656 šš8.135 š1.00 š0.00
> šATOM šš3311 šH5 šRES šš211 ššššš12.695 š-7.553 šš9.185 š1.00 š0.00
> šATOM šš3312 šC4 šRES šš211 ššššš13.722 š-8.746 šš7.726 š1.00 š0.00
>
> šAnswers in mailing list were not helpful until so far as this is not water and TER records look ok and šfile was not from tleap. Maybe file of ligand used for antechamber with all hydrogens was, I ll check that if that can be relevant.
>
> šBest regards,
> šAndrew
> š02.11.2011, 09:36, "Jason Swails" <jason.swails.gmail.com>:
>> ššI've seen tleap do very weird things determining the ATOMS_PER_MOLECULE and
>> ššSOLVENT_POINTERS section of the topology file, so I KNOW there's a bug
>> ššthere for some corner cases (that are becoming more common). šRoss can
>> ššattest to this as well -- it has caused weird segfaults in pmemd and sander
>> ššwith strange systems that we've both looked into.
>>
>> ššThat's why I added a function in my prmtop editor (parmed) to reset this
>> ššsection completely based on the actual bonded atom network. šObviously not
>> ššas ideal as fixing it in leap itself, but it's a quick way of testing
>> ššwhether or not this will fix the issue...
>>
>> šš(The parmed command is "setMolecules solute_ions=True" if you were
>> ššinterested in trying this to see if it fixes the issue)
>>
>> ššAll the best,
>> ššJason
>>
>> ššOn Tue, Nov 1, 2011 at 9:48 PM, case <case.biomaps.rutgers.edu> wrote:
>>> šššOn Tue, Nov 01, 2011, Breuer, Marian wrote:
>>>>> šššI'm currently trying to carry out MD simulations with sander (MPI
>>>>> šššparallel version, AMBER11) on a protein system using SHAKE bond
>>>>> šššconstraints for bonds containing hydrogen (sander option ntc=2). These
>>>>> šššwork with up to 14 processors, but with any number of cores higher than
>>>>> šššthat the simulations abort in the first step with the error message:
>>>>>
>>>>> ššššpartition error in shake on processor ššššššššššš0
>>>>> ššššthis processor has atoms ššššššššššš1 šthrough šššššššš8265
>>>>> ššššatom šššššššš8265 is within this range
>>>>> ššššatom šššššššš8266 is not within this range !
>>> šššOK: your prmtop file has bad information in it, so the "problem" is not
>>> šššwith
>>> šššsander, but with how the prmtop file itself was generated.
>>>
>>> šššSpecifically, the ATOMS_PER_MOLECULE field in the prmtop has this:
>>>
>>> ššš%FLAG ATOMS_PER_MOLECULE
>>> ššš%FORMAT(10I8)
>>> šššššš8265 šššš848 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1
>>>
>>> ššš...etc., which is the reason that sander thinks that atoms 8265 and 8266
>>> šššare
>>> šššin different molecules (and hence can be assigned to different processors).
>>>
>>> šššYou seem to have a system with 1 "HER" group, 9 heme groups, a protein,
>>> šššand a pile of sodiums, chlorides and water. šIt looks like at some point,
>>> šššthe HER and HEM residues had their coordinates after the regular protein
>>> šššcoordinates, but that at some point, these HER/HEM atoms got placed before
>>> šššthe protein ones. šAlso, most likely, each HEM group should be its own
>>> šššmolecule (which is later cross=linked to the protein somehow. šThis means
>>> šššthat in the input pdb file, there should have been a TER after the protein
>>> šššatoms and after each HEM/HER residue. šThen (once all hydrogens are added)
>>> šššthe first 8265 atoms would be protein (amino acid atoms); there should
>>> šššthen be 10 HER/HEM residues. šThe ions and water would then be added by
>>> šššLEaP.
>>>
>>> šššMy wild guess is that either your input pdb file didn't have TER cards in
>>> šššall
>>> šššthe required places, or that you used the savePdb command at some point,
>>> šššthen
>>> šššre-read that back into LEaP(?) It may well be a bug in LEaP and not
>>> šššoperator
>>> šššerror, but I can't tell.
>>>
>>> šššBut this is about as far as I can go...if seeing this description of the
>>> šššproblem doesn't help, we would need to know the exact commands you used to
>>> šššcreate the prmtop file.
>>>
>>> ššš...good luck...dac
>>>
>>> ššš_______________________________________________
>>> šššAMBER mailing list
>>> šššAMBER.ambermd.org
>>> šššhttp://lists.ambermd.org/mailman/listinfo/amber
>> šš--
>> ššJason M. Swails
>> ššQuantum Theory Project,
>> ššUniversity of Florida
>> ššPh.D. Candidate
>> šš352-392-4032
>> šš_______________________________________________
>> ššAMBER mailing list
>> ššAMBER.ambermd.org
>> ššhttp://lists.ambermd.org/mailman/listinfo/amber
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