Dear Justin, These parameters are present in literature. I think these bonds/parameters are correctly generated. You said "The previous topology output suggests not, because ZN is not renamed to ZNW". I do not know what to do.
I added the OZ-HZ bond in ffbonded.itp. Unfortunately I get the same errors: ERROR 1 [file protein_Ion_chain_A2.itp, line 33]: No default Bond types ERROR 2 [file protein_Ion_chain_A2.itp, line 34]: No default Bond types ffbonded.itp: Zn NA 1 0.20500 16744.0 ;modified Zn NB 1 0.20500 16744.0 ;modified Zn OZ 1 0.23000 16744.0 ;modified OZ HZ 1 0.09572 221682.2 ;modified 2014-04-04 16:29 GMT+03:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/4/14, 9:25 AM, Ahmet yıldırım wrote: > >> Dear Justin, >> >> Firstly, I renamed HETATM 2068 O HOH A1001 in pdb. This water is bound >> to >> Zn. >> its new name: >> HETATM 2068 OZ OWZ A1001 >> >> Zn is bound to three Histidine atoms (two NE2 atoms and one ND1 atom) and >> a >> water molecule in carbonic anhydrase as I said before. I did the following >> changes on amber99sb-ildn. What do you suggestion? >> >> specbond.dat: >> 11 >> .. >> HIS ND1 1 ZN Zn 1 0.205 HIDZ ZNW >> ;modified >> HIS NE2 1 ZN Zn 1 0.205 HIEZ ZNW >> ;modified >> OWZ OZ 1 ZN Zn 1 0.23 ZOH2 ZNW >> ;modified >> >> > Are these bonds correctly generated? The previous topology output > suggests not, because ZN is not renamed to ZNW. > > > residuetypes.dat: >> ZNW Ion ;modified >> ZOH2 water ;modified >> OWZ water ;modified >> HIDZ Protein >> HIEZ Protein >> >> aminoacids.hdb: >> OWZ 1 ;modified >> 2 7 HZ OZ >> .. >> HIDZ 6 >> 1 1 H N -C CA >> 1 5 HA CA N CB C >> 2 6 HB CB CA CG >> 1 1 HD1 ND1 CG CE1 >> 1 1 HE1 CE1 ND1 NE2 >> 1 1 HD2 CD2 CG NE2 >> HIEZ 6 >> 1 1 H N -C CA >> 1 5 HA CA N CB C >> 2 6 HB CB CA CG >> 1 1 HE1 CE1 ND1 NE2 >> 1 1 HE2 NE2 CE1 CD2 >> 1 1 HD2 CD2 CG NE2 >> >> aminoacids.rtp: >> [ ZNW ];modified >> [ atoms ] >> ZN Zn 0.89230 1 >> >> [ ZOH2 ];modified >> [ atoms ] >> OZ OZ -0.8824 0 >> HZ1 HZ 0.5001 0 >> HZ2 HZ 0.5001 0 >> [ bonds ] >> OZ HZ1 >> OZ HZ2 >> >> [ OWZ ];modified >> [ atoms ] >> OZ OZ -0.8824 0 >> HZ1 HZ 0.5001 0 >> HZ2 HZ 0.5001 0 >> [ bonds ] >> OZ HZ1 >> OZ HZ2 >> [ HIDZ ];modified >> [ atoms ] >> N N -0.41570 1 >> H H 0.27190 2 >> CA CT 0.01880 3 >> HA H1 0.08810 4 >> CB CT -0.04620 5 >> HB1 HC 0.04020 6 >> HB2 HC 0.04020 7 >> CG CC -0.02660 8 >> ND1 NA -0.38110 9 >> HD1 H 0.36490 10 >> CE1 CR 0.20570 11 >> HE1 H5 0.13920 12 >> NE2 NB -0.57270 13 >> CD2 CV 0.12920 14 >> HD2 H4 0.11470 15 >> C C 0.59730 16 >> O O -0.56790 17 >> [ bonds ] >> N H >> N CA >> CA HA >> CA CB >> CA C >> CB HB1 >> CB HB2 >> CB CG >> CG ND1 >> CG CD2 >> ND1 HD1 >> ND1 CE1 >> CE1 HE1 >> CE1 NE2 >> NE2 CD2 >> CD2 HD2 >> C O >> -C N >> [ impropers ] >> -C CA N H >> CA +N C O >> CG CE1 ND1 HD1 >> CG NE2 CD2 HD2 >> ND1 NE2 CE1 HE1 >> ND1 CD2 CG CB >> >> [ HIEZ ];modified >> [ atoms ] >> N N -0.41570 1 >> H H 0.27190 2 >> CA CT -0.05810 3 >> HA H1 0.13600 4 >> CB CT -0.00740 5 >> HB1 HC 0.03670 6 >> HB2 HC 0.03670 7 >> CG CC 0.18680 8 >> ND1 NB -0.54320 9 >> CE1 CR 0.16350 10 >> HE1 H5 0.14350 11 >> NE2 NA -0.27950 12 >> HE2 H 0.33390 13 >> CD2 CW -0.22070 14 >> HD2 H4 0.18620 15 >> C C 0.59730 16 >> O O -0.56790 17 >> [ bonds ] >> N H >> N CA >> CA HA >> CA CB >> CA C >> CB HB2 >> CB HB1 >> CB CG >> CG ND1 >> CG CD2 >> ND1 CE1 >> CE1 HE1 >> CE1 NE2 >> NE2 HE2 >> NE2 CD2 >> CD2 HD2 >> C O >> -C N >> [ impropers ] >> -C CA N H >> CA +N C O >> CE1 CD2 NE2 HE2 >> CG NE2 CD2 HD2 >> ND1 NE2 CE1 HE1 >> ND1 CD2 CG CB >> >> atomtypes.atp: >> OZ 16.00000 ; modified >> HZ 1.00800 ; modified >> >> ffbonded.itp: >> [ bondtypes ] >> Zn NA 1 0.20500 16744.0 ;modified >> Zn NB 1 0.20500 16744.0 ;modified >> Zn OZ 1 0.23000 16744.0 ;modified >> > > You get the fatal error about missing bond types because you haven't > defined the OZ-HZ bond here. > > -Justin > > > [ angletypes ] >> HW OW HW 1 104.5 142.490 ; TIP3P water ;modified >> >> CR NA Zn 1 126.0 83.720 ;modified >> CW NB Zn 1 126.0 83.720 ;modified >> NA Zn NB 1 109.5 96.278 ;modified >> NB Zn NB 1 109.5 96.278 ;modified >> NA Zn OZ 1 109.5 96.278 ;modified >> NB Zn OZ 1 109.5 96.278 ;modified >> Zn OZ HZ 1 124.0 83.720 ;modified >> HZ OZ HZ 1 104.5 4186.000 ;modified >> >> [ dihedraltypes ] >> X Zn NA X 9 0.0 0.00000 3 ;modified >> X Zn NB X 9 0.0 0.00000 3 ;modified >> X Zn OZ X 9 0.0 0.00000 3 ;modified >> >> ffnonbonded.itp: >> OW 8 16.00 0.0000 A 1.76820e-01 6.371092e-01 >> ;modified >> OZ 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 >> ;modified >> HZ 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 >> ;modified >> Zn 30 65.4 0.0000 A 1.10000e-01 5.23250e-02 >> ;modified >> >> >> 2014-04-04 15:51 GMT+03:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 4/4/14, 8:47 AM, Ahmet yıldırım wrote: >>> >>> Hi, >>>> >>>> The bond types are set properly in ffbonded.itp. But I get the following >>>> errors after grompp command. How can I fix it? >>>> ERROR 1 [file protein_Ion_chain_A2.itp, line 33]: >>>> No default Bond types >>>> >>>> >>>> ERROR 2 [file protein_Ion_chain_A2.itp, line 34]: >>>> No default Bond types >>>> >>>> protein_Ion_chain_A2.itp: >>>> [ moleculetype ] >>>> ; Name nrexcl >>>> Ion_chain_A2 3 >>>> >>>> [ atoms ] >>>> ; nr type resnr residue atom cgnr charge mass >>>> typeB chargeB massB >>>> ; residue 262 ZN rtp ZN q +2.0 >>>> 1 Zn 262 ZN ZN 1 2 65.4 >>>> ; >>>> qtot 2 >>>> >>>> >>> If I'm remembering your model right, the Zn-HOH complex doesn't bear a +2 >>> charge on Zn. Is this what you actually want? >>> >>> >>> ; residue 1001 OWZ rtp OWZ q +0.1 >>> >>>> 2 OZ 1001 OWZ OZ 2 -0.8824 16 >>>> ; >>>> qtot 1.118 >>>> 3 HZ 1001 OWZ HZ1 2 0.5001 1.008 >>>> ; >>>> qtot 1.618 >>>> 4 HZ 1001 OWZ HZ2 2 0.5001 1.008 >>>> ; >>>> qtot 2.118 >>>> >>>> [ bonds ] >>>> ; ai aj funct c0 c1 c2 >>>> c3 >>>> 2 3 1 >>>> 2 4 1 >>>> >>>> >>>> Apparently whatever ffbonded.itp file that is being read doesn't have >>> these parameters. Unfortunately, there's not enough information to say >>> why. If OZ-HZ parameters were there, there would be no reason they >>> wouldn't be read. >>> >>> -Justin >>> >>> >>> [ angles ] >>> >>>> ; ai aj ak funct c0 c1 >>>> c2 c3 >>>> 3 2 4 1 >>>> >>>> ; Include Position restraint file >>>> #ifdef POSRES >>>> #include "posre_Ion_chain_A2.itp" >>>> #endif >>>> >>>> >>>> >>>> >>>> >>>> 2014-04-04 0:32 GMT+03:00 Justin Lemkul <jalem...@vt.edu>: >>>> >>>> >>>> >>>>> On 4/3/14, 2:58 PM, Gmail2 wrote: >>>>> >>>>> Dear Justin, >>>>> >>>>>> >>>>>> Zn bound to three Histidine atoms and a water in carbonic anhydrase. >>>>>> This >>>>>> water bound to Zn has different parameters than solvent water. That >>>>>> parameters is present in literature. How should I set up such a >>>>>> system? >>>>>> >>>>>> PS: I will use 'pdb2gmx' with -vsite hydrogens. >>>>>> >>>>>> >>>>>> If you need virtual sites, then you need to figure out how to >>>>>> properly >>>>>> >>>>> build a virtual site database entry for that particular type of >>>>> molecule. >>>>> That's entirely separate from any of the force field parameters >>>>> you've >>>>> shown before, but realize that doing so negates most of the Zn-HOH >>>>> bonded >>>>> parameters you posted. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> -- >>>>> ================================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>> >>>>> Department of Pharmaceutical Sciences >>>>> School of Pharmacy >>>>> Health Sciences Facility II, Room 601 >>>>> University of Maryland, Baltimore >>>>> 20 Penn St. >>>>> Baltimore, MD 21201 >>>>> >>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>> http://mackerell.umaryland.edu/~jalemkul >>>>> >>>>> ================================================== >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at http://www.gromacs.org/ >>>>> Support/Mailing_Lists/GMX-Users_List before posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >>> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Ahmet Yıldırım -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.