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 3308 O GLU 210 58.563 30.137 20.807 1.00 0.00 O
ATOM 3309 OXT GLU 210 59.202 29.891 18.732 1.00 0.00 O
ATOM 3310 C6 RES 211 47.114 26.505 42.295 1.00 0.00 C
TER
ATOM 3311 H5 RES 211 46.856 26.607 43.346 1.00 0.00 H
ATOM 3312 C4 RES 211 47.882 25.415 41.887 1.00 0.00 C
ATOM 3313 H3 RES 211 48.209 24.689 42.629 1.00 0.00 H
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 1685 C GLU 210 23.190 20.522 4.241 1.00 0.00 C
ATOM 1686 O GLU 210 23.659 21.648 3.992 1.00 0.00 O
ATOM 1687 OXT GLU 210 23.806 19.469 3.926 1.00 0.00 O
TER 1688 GLU 210
HETATM 1689 C1 RES 211 23.181 41.843 13.592 1.00 0.00 C
HETATM 1690 C2 RES 211 14.795 45.766 16.068 1.00 0.00 C
HETATM 1691 C3 RES 211 15.158 46.148 17.360 1.00 0.00 C
HETATM 1692 C4 RES 211 22.058 43.937 13.012 1.00 0.00 C
HETATM 1693 C5 RES 211 21.049 41.831 12.394 1.00 0.00 C
HETATM 1694 C6 RES 211 20.991 44.620 12.429 1.00 0.00 C
so there it was not separated.
Best regards,
Andrew
26.11.2011, 12:38, "Andrew Voronkov" <drugdesign.yandex.ru>:
> I have now the same issue with small molecule ligand docked into zinc containing atom.
> TER record are šok and PDB was not generated by tleap.
>
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> šusing šš5000.0 points per unit in tabled values
> šTESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = šš0.2738E-14 ššat šš2.422500
> | CHECK d/dx switch(x): max rel err = šš0.8314E-11 ššat šš2.736960
> š---------------------------------------------------
> | Local SIZE OF NONBOND LIST = šššš524773
> | TOTAL SIZE OF NONBOND LIST = ššš3783691
> špartition error in shake on processor ššššššššššš0
> šthis processor has atoms ššššššššššš1 šthrough šššššššš3310
> šatom šššššššš3310 is within this range
> šatom šššššššš3311 is not within this range !
>
> ATOM šš3310 šC6 šRES šš211 ššššš12.953 š-7.656 šš8.135 š1.00 š0.00
> ATOM šš3311 šH5 šRES šš211 ššššš12.695 š-7.553 šš9.185 š1.00 š0.00
> ATOM šš3312 šC4 šRES šš211 ššššš13.722 š-8.746 šš7.726 š1.00 š0.00
>
> Answers 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.
>
> Best regards,
> Andrew
> 02.11.2011, 09:36, "Jason Swails" <jason.swails.gmail.com>:
>
>> šI've seen tleap do very weird things determining the ATOMS_PER_MOLECULE and
>> šSOLVENT_POINTERS section of the topology file, so I KNOW there's a bug
>> šthere for some corner cases (that are becoming more common). šRoss can
>> šattest to this as well -- it has caused weird segfaults in pmemd and sander
>> šwith strange systems that we've both looked into.
>>
>> šThat's why I added a function in my prmtop editor (parmed) to reset this
>> šsection completely based on the actual bonded atom network. šObviously not
>> šas ideal as fixing it in leap itself, but it's a quick way of testing
>> šwhether or not this will fix the issue...
>>
>> š(The parmed command is "setMolecules solute_ions=True" if you were
>> šinterested in trying this to see if it fixes the issue)
>>
>> šAll the best,
>> šJason
>>
>> šOn Tue, Nov 1, 2011 at 9:48 PM, case <case.biomaps.rutgers.edu> wrote:
>>> ššOn Tue, Nov 01, 2011, Breuer, Marian wrote:
>>>>> ššI'm currently trying to carry out MD simulations with sander (MPI
>>>>> ššparallel version, AMBER11) on a protein system using SHAKE bond
>>>>> ššconstraints for bonds containing hydrogen (sander option ntc=2). These
>>>>> ššwork with up to 14 processors, but with any number of cores higher than
>>>>> ššthat the simulations abort in the first step with the error message:
>>>>>
>>>>> šššpartition error in shake on processor ššššššššššš0
>>>>> šššthis processor has atoms ššššššššššš1 šthrough šššššššš8265
>>>>> šššatom šššššššš8265 is within this range
>>>>> šššatom šššššššš8266 is not within this range !
>>> ššOK: your prmtop file has bad information in it, so the "problem" is not
>>> ššwith
>>> ššsander, but with how the prmtop file itself was generated.
>>>
>>> ššSpecifically, the ATOMS_PER_MOLECULE field in the prmtop has this:
>>>
>>> šš%FLAG ATOMS_PER_MOLECULE
>>> šš%FORMAT(10I8)
>>> ššššš8265 šššš848 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1
>>>
>>> šš...etc., which is the reason that sander thinks that atoms 8265 and 8266
>>> ššare
>>> ššin different molecules (and hence can be assigned to different processors).
>>>
>>> ššYou seem to have a system with 1 "HER" group, 9 heme groups, a protein,
>>> ššand a pile of sodiums, chlorides and water. šIt looks like at some point,
>>> ššthe HER and HEM residues had their coordinates after the regular protein
>>> ššcoordinates, but that at some point, these HER/HEM atoms got placed before
>>> ššthe protein ones. šAlso, most likely, each HEM group should be its own
>>> ššmolecule (which is later cross=linked to the protein somehow. šThis means
>>> ššthat in the input pdb file, there should have been a TER after the protein
>>> ššatoms and after each HEM/HER residue. šThen (once all hydrogens are added)
>>> ššthe first 8265 atoms would be protein (amino acid atoms); there should
>>> ššthen be 10 HER/HEM residues. šThe ions and water would then be added by
>>> ššLEaP.
>>>
>>> ššMy wild guess is that either your input pdb file didn't have TER cards in
>>> ššall
>>> ššthe required places, or that you used the savePdb command at some point,
>>> ššthen
>>> ššre-read that back into LEaP(?) It may well be a bug in LEaP and not
>>> ššoperator
>>> ššerror, but I can't tell.
>>>
>>> ššBut this is about as far as I can go...if seeing this description of the
>>> ššproblem doesn't help, we would need to know the exact commands you used to
>>> ššcreate the prmtop file.
>>>
>>> šš...good luck...dac
>>>
>>> šš_______________________________________________
>>> ššAMBER mailing list
>>> ššAMBER.ambermd.org
>>> ššhttp://lists.ambermd.org/mailman/listinfo/amber
>> š--
>> šJason M. Swails
>> šQuantum Theory Project,
>> šUniversity of Florida
>> šPh.D. Candidate
>> š352-392-4032
>> š_______________________________________________
>> šAMBER mailing list
>> šAMBER.ambermd.org
>> šhttp://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Nov 26 2011 - 10:00:03 PST
