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
>
>-------- Пересылаемое сообщение --------
>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 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 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). 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Nov 26 2011 - 12:30:04 PST
