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-- Yong Duan, Ph.D, Professor UC Davis Genome Center and Department of Biomedical Engineering University of California at Davis Davis, CA 95616 530-754-7632 On 11/27/11 1:00 AM, "Andrew Voronkov" <drugdesign.yandex.ru> wrote: >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 >>> >>> -------- 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 >>> -------- Завершение пересылаемого сообщения -------- >>> >>> _______________________________________________ >>> 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 > >_______________________________________________ >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/amberReceived on Sun Nov 27 2011 - 11:30:02 PST