I have tried two approaches to add hydrogens. One was omega2 with force field MMFF94.
Another was Discovery Studio visualizer, which uses CHARMMm force field.
The main differences between initial PDB and file ambpdb are shown below.
I have used ligand molecule with all hydrogens for antechamber and then PDB with protein, ligand and and zinc with removed hydrogens.
What is the best way to add hydrogens in order to not get such errors? Without zinc atom, the procedures described above work fine for protein-ligand complexes, may zinc atom bound and parametrized in ZAFF affect parametrization in such way?
Best regards,
Andrew
27.11.2011, 00:28, "Yong Duan" <duan.ucdavis.edu>:
> Can you also post the savepdb result here, just curious ...
> By the way, how did you assign the hydrogens?
>
> yong
>
> On 11/26/11 12:22 PM, "Andrew Voronkov" <drugdesign.yandex.ru> wrote:
>
>> 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
>>
>> -------- ðÅÒÅÓÙÌÁÅÍÏÅ ÓÏÏÂÝÅÎÉÅ š--------
>> 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
>> šššO
>> ATOM šš3309 šOXT GLU šš210 ššššš59.202 š29.891 š18.732 š1.00 š0.00
>> šššO
>> ATOM šš3310 šC6 šRES šš211 ššššš47.114 š26.505 š42.295 š1.00 š0.00
>> šššC
>> TER
>> ATOM šš3311 šH5 šRES šš211 ššššš46.856 š26.607 š43.346 š1.00 š0.00
>> šššH
>> ATOM šš3312 šC4 šRES šš211 ššššš47.882 š25.415 š41.887 š1.00 š0.00
>> šššC
>> ATOM šš3313 šH3 šRES šš211 ššššš48.209 š24.689 š42.629 š1.00 š0.00
>> šššH
>>
>> 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
>> šššC
>> ATOM šš1686 šO ššGLU šš210 ššššš23.659 š21.648 šš3.992 š1.00 š0.00
>> šššO
>> ATOM šš1687 šOXT GLU šš210 ššššš23.806 š19.469 šš3.926 š1.00 š0.00
>> šššO
>> TER ššš1688 šššššGLU šš210
>> HETATM 1689 šC1 šRES šš211 ššššš23.181 š41.843 š13.592 š1.00 š0.00
>> šššC
>> HETATM 1690 šC2 šRES šš211 ššššš14.795 š45.766 š16.068 š1.00 š0.00
>> šššC
>> HETATM 1691 šC3 šRES šš211 ššššš15.158 š46.148 š17.360 š1.00 š0.00
>> šššC
>> HETATM 1692 šC4 šRES šš211 ššššš22.058 š43.937 š13.012 š1.00 š0.00
>> šššC
>> HETATM 1693 šC5 šRES šš211 ššššš21.049 š41.831 š12.394 š1.00 š0.00
>> šššC
>> HETATM 1694 šC6 šRES šš211 ššššš20.991 š44.620 š12.429 š1.00 š0.00
>> šššC
>>
>> so there it was not separated.
>>
>> Best regards,
>> Andrew
>>
>> 26.11.2011, 12:38, "Andrew Voronkov" <drugdesign.yandex.ru>:
>>> ššI have now the same issue with small molecule ligand docked into zinc
>>> containing atom.
>>> ššTER record are šok and PDB was not generated by tleap.
>>>
>>> ššAPPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>>> šššusing šš5000.0 points per unit in tabled values
>>> šššTESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>>> šš| CHECK switch(x): max rel err = šš0.2738E-14 ššat šš2.422500
>>> šš| CHECK d/dx switch(x): max rel err = šš0.8314E-11 ššat šš2.736960
>>> ššš---------------------------------------------------
>>> šš| Local SIZE OF NONBOND LIST = šššš524773
>>> šš| TOTAL SIZE OF NONBOND LIST = ššš3783691
>>> šššpartition error in shake on processor ššššššššššš0
>>> šššthis processor has atoms ššššššššššš1 šthrough šššššššš3310
>>> šššatom šššššššš3310 is within this range
>>> šššatom šššššššš3311 is not within this range !
>>>
>>> ššATOM šš3310 šC6 šRES šš211 ššššš12.953 š-7.656 šš8.135 š1.00 š0.00
>>> ššATOM šš3311 šH5 šRES šš211 ššššš12.695 š-7.553 šš9.185 š1.00 š0.00
>>> ššATOM šš3312 šC4 šRES šš211 ššššš13.722 š-8.746 šš7.726 š1.00 š0.00
>>>
>>> ššAnswers 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.
>>>
>>> ššBest regards,
>>> ššAndrew
>>> šš02.11.2011, 09:36, "Jason Swails" <jason.swails.gmail.com>:
>>>> šššI've seen tleap do very weird things determining the
>>>> ATOMS_PER_MOLECULE and
>>>> šššSOLVENT_POINTERS section of the topology file, so I KNOW there's a
>>>> bug
>>>> šššthere for some corner cases (that are becoming more common). šRoss
>>>> can
>>>> šššattest to this as well -- it has caused weird segfaults in pmemd and
>>>> sander
>>>> šššwith strange systems that we've both looked into.
>>>>
>>>> šššThat's why I added a function in my prmtop editor (parmed) to reset
>>>> this
>>>> šššsection completely based on the actual bonded atom network.
>>>> Obviously not
>>>> šššas ideal as fixing it in leap itself, but it's a quick way of testing
>>>> šššwhether or not this will fix the issue...
>>>>
>>>> ššš(The parmed command is "setMolecules solute_ions=True" if you were
>>>> šššinterested in trying this to see if it fixes the issue)
>>>>
>>>> šššAll the best,
>>>> šššJason
>>>>
>>>> šššOn Tue, Nov 1, 2011 at 9:48 PM, case <case.biomaps.rutgers.edu>
>>>> wrote:
>>>>> ššššOn Tue, Nov 01, 2011, Breuer, Marian wrote:
>>>>>>> ššššI'm currently trying to carry out MD simulations with sander (MPI
>>>>>>> ššššparallel version, AMBER11) on a protein system using SHAKE bond
>>>>>>> ššššconstraints for bonds containing hydrogen (sander option ntc=2).
>>>>>>> These
>>>>>>> ššššwork with up to 14 processors, but with any number of cores
>>>>>>> higher than
>>>>>>> ššššthat the simulations abort in the first step with the error
>>>>>>> message:
>>>>>>>
>>>>>>> šššššpartition error in shake on processor ššššššššššš0
>>>>>>> šššššthis processor has atoms ššššššššššš1 šthrough šššššššš8265
>>>>>>> šššššatom šššššššš8265 is within this range
>>>>>>> šššššatom šššššššš8266 is not within this range !
>>>>> ššššOK: your prmtop file has bad information in it, so the "problem"
>>>>> is not
>>>>> ššššwith
>>>>> ššššsander, but with how the prmtop file itself was generated.
>>>>>
>>>>> ššššSpecifically, the ATOMS_PER_MOLECULE field in the prmtop has this:
>>>>>
>>>>> šššš%FLAG ATOMS_PER_MOLECULE
>>>>> šššš%FORMAT(10I8)
>>>>> ššššššš8265 šššš848 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1 šššššš1
>>>>> ššš1
>>>>>
>>>>> šššš...etc., which is the reason that sander thinks that atoms 8265
>>>>> and 8266
>>>>> ššššare
>>>>> ššššin different molecules (and hence can be assigned to different
>>>>> processors).
>>>>>
>>>>> ššššYou seem to have a system with 1 "HER" group, 9 heme groups, a
>>>>> protein,
>>>>> ššššand a pile of sodiums, chlorides and water. šIt looks like at some
>>>>> point,
>>>>> ššššthe HER and HEM residues had their coordinates after the regular
>>>>> protein
>>>>> ššššcoordinates, but that at some point, these HER/HEM atoms got
>>>>> placed before
>>>>> ššššthe protein ones. šAlso, most likely, each HEM group should be its
>>>>> own
>>>>> ššššmolecule (which is later cross=linked to the protein somehow.
>>>>> This means
>>>>> ššššthat in the input pdb file, there should have been a TER after the
>>>>> protein
>>>>> ššššatoms and after each HEM/HER residue. šThen (once all hydrogens
>>>>> are added)
>>>>> ššššthe first 8265 atoms would be protein (amino acid atoms); there
>>>>> should
>>>>> ššššthen be 10 HER/HEM residues. šThe ions and water would then be
>>>>> added by
>>>>> ššššLEaP.
>>>>>
>>>>> ššššMy wild guess is that either your input pdb file didn't have TER
>>>>> cards in
>>>>> ššššall
>>>>> ššššthe required places, or that you used the savePdb command at some
>>>>> point,
>>>>> ššššthen
>>>>> ššššre-read that back into LEaP(?) It may well be a bug in LEaP and not
>>>>> ššššoperator
>>>>> ššššerror, but I can't tell.
>>>>>
>>>>> ššššBut this is about as far as I can go...if seeing this description
>>>>> of the
>>>>> ššššproblem doesn't help, we would need to know the exact commands you
>>>>> used to
>>>>> ššššcreate the prmtop file.
>>>>>
>>>>> šššš...good luck...dac
>>>>>
>>>>> šššš_______________________________________________
>>>>> ššššAMBER mailing list
>>>>> ššššAMBER.ambermd.org
>>>>> ššššhttp://lists.ambermd.org/mailman/listinfo/amber
>>>> ššš--
>>>> šššJason M. Swails
>>>> šššQuantum Theory Project,
>>>> šššUniversity of Florida
>>>> šššPh.D. Candidate
>>>> ššš352-392-4032
>>>> ššš_______________________________________________
>>>> šššAMBER mailing list
>>>> šššAMBER.ambermd.org
>>>> šššhttp://lists.ambermd.org/mailman/listinfo/amber
>> -------- úÁ×ÅÒÛÅÎÉÅ ÐÅÒÅÓÙÌÁÅÍÏÇÏ ÓÏÏÂÝÅÎÉÑ --------
>>
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Received on Sun Nov 27 2011 - 01:30:02 PST
