I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but after processing that structure to grompp I've obtained errors like
ERROR 1 [file topol.top, line 2106]: No default Bond types ERROR 2 [file topol.top, line 2144]: No default Bond types ERROR 3 [file topol.top, line 3153]: No default Bond types ERROR 4 [file topol.top, line 8725]: No default U-B types ERROR 5 [file topol.top, line 8792]: No default U-B types ERROR 6 [file topol.top, line 10624]: No default U-B types ERROR 7 [file topol.top, line 10625]: No default U-B types ERROR 8 [file topol.top, line 11382]: No default U-B types ERROR 9 [file topol.top, line 11383]: No default U-B types ERROR 10 [file topol.top, line 11384]: No default U-B types ERROR 11 [file topol.top, line 11385]: No default U-B types ERROR 12 [file topol.top, line 11491]: No default U-B types ERROR 13 [file topol.top, line 11492]: No default U-B types ERROR 14 [file topol.top, line 11493]: No default U-B types ERROR 15 [file topol.top, line 11506]: No default U-B types ERROR 16 [file topol.top, line 11507]: No default U-B types ERROR 17 [file topol.top, line 11508]: No default U-B types ERROR 18 [file topol.top, line 12147]: No default Proper Dih. types ERROR 19 [file topol.top, line 12148]: No default Proper Dih. types ERROR 20 [file topol.top, line 12149]: No default Proper Dih. types ERROR 21 [file topol.top, line 12150]: No default Proper Dih. types ERROR 22 [file topol.top, line 12151]: No default Proper Dih. types ERROR 23 [file topol.top, line 12152]: No default Proper Dih. types ERROR 24 [file topol.top, line 12247]: No default Proper Dih. types ERROR 25 [file topol.top, line 12248]: No default Proper Dih. types ERROR 26 [file topol.top, line 12249]: No default Proper Dih. types ERROR 27 [file topol.top, line 12250]: No default Proper Dih. types ERROR 28 [file topol.top, line 12251]: No default Proper Dih. types ERROR 29 [file topol.top, line 12252]: No default Proper Dih. types ERROR 30 [file topol.top, line 14948]: No default Proper Dih. types ERROR 31 [file topol.top, line 14950]: No default Proper Dih. types ERROR 32 [file topol.top, line 14952]: No default Proper Dih. types ERROR 33 [file topol.top, line 14956]: No default Proper Dih. types ERROR 34 [file topol.top, line 14957]: No default Proper Dih. types ERROR 35 [file topol.top, line 14958]: No default Proper Dih. types ERROR 36 [file topol.top, line 14959]: No default Proper Dih. types ERROR 37 [file topol.top, line 14960]: No default Proper Dih. types ERROR 38 [file topol.top, line 14961]: No default Proper Dih. types ERROR 39 [file topol.top, line 14962]: No default Proper Dih. types ERROR 40 [file topol.top, line 14963]: No default Proper Dih. types ERROR 41 [file topol.top, line 14964]: No default Proper Dih. types ERROR 42 [file topol.top, line 14965]: No default Proper Dih. types ERROR 43 [file topol.top, line 14966]: No default Proper Dih. types ERROR 44 [file topol.top, line 16263]: No default Proper Dih. types ERROR 45 [file topol.top, line 16264]: No default Proper Dih. types ERROR 46 [file topol.top, line 16269]: No default Proper Dih. types ERROR 47 [file topol.top, line 16270]: No default Proper Dih. types Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 3 [file topol.top, line 16745]: System has non-zero total charge: 7.000001 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. ------------------------------------------------------- Program grompp, VERSION 4.6 Source code file: /home/own/Documents/distr/gromacs-4.6/src/kernel/grompp.c, line: 1593 Fatal error: There were 47 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors During visualization of the complex.gro file I didnt observe any distortions in the geometry of heme-cytochrome complex (it looks like NMR structure) but why that errors occured ? James 2013/4/3 James Starlight <jmsstarli...@gmail.com> > sorry it was mistake :) > > assuming that heme is covalently bonded to the cytochrome by means of 2 > cysteines how should I define such bindings (assuming that heme is part of > my protein) based onb the charmm parameters ? > its not clear for me why such connection is absent in the residue.dat > (having HEME included in the rtps) > > I still need a example of properly parametrized hem complexed with any > cytochrome :) > > James > > > 2013/4/3 James Starlight <jmsstarli...@gmail.com> > >> hmm >> >> I've done parametrization of the hem using standart charmm36 parameters >> but indeed there is some confusing with the hydrogens >> >> for example my pdb (obtained from NMR structure) consist of 2 extra >> hydrogens (which both parts of the methyl groups) which are not present in >> the rtp parameters. So if I delete both of that hydrogens from pdb- my HEM >> will be -2 charged. On tyhe other hands hem in my pdb lack of 2 protons in >> the COOH groups. Could someone provide me with the HEM (in planargeometry) >> parametrized in charmm36 ? >> >> By the way assuming that the HEM itself is not covalently bonded to the >> rest of the protein ( as in the case of GFP or rhodopsin). So the >> parameters for the hem should be included as the any other diffusiable >> ligand (as the separate itp file) in topology, should'n it? >> >> James >> >> >> >> 2013/4/3 Justin Lemkul <jalem...@vt.edu> >> >>> On Wed, Apr 3, 2013 at 8:24 AM, James Starlight <jmsstarli...@gmail.com >>> >wrote: >>> >>> > Dear Gromacs users! >>> > >>> > >>> > I want to simulate Cytochrome C in complex with HEM using NMR full-atom >>> > structure of that protein as the starting conformation and charm36 >>> force >>> > field's parameters. >>> > >>> > in the charm36 ff I've found parameters for HEM but I have not found >>> params >>> > for the hydrogens (in the aminoacids.hdb file) as well as definition >>> of the >>> > HEM as the part of the protein in the residuetypes.dat ( including >>> > connection to the rest of polypeptide chain ). >>> > >>> > So during pdb2gmx parametrisation I've obtained errors like >>> > >>> > WARNING: atom HA is missing in residue HEME 105 in the pdb file >>> > You might need to add atom HA to the hydrogen database of >>> building >>> > block HEME >>> > in the file aminoacids.hdb (see the manual) >>> > >>> > >>> > WARNING: atom HB is missing in residue HEME 105 in the pdb file >>> > You might need to add atom HB to the hydrogen database of >>> building >>> > block HEME >>> > in the file aminoacids.hdb (see the manual) >>> > >>> > >>> > WARNING: atom HC is missing in residue HEME 105 in the pdb file >>> > You might need to add atom HC to the hydrogen database of >>> building >>> > block HEME >>> > in the file aminoacids.hdb (see the manual) >>> > >>> > >>> > WARNING: atom HD is missing in residue HEME 105 in the pdb file >>> > You might need to add atom HD to the hydrogen database of >>> building >>> > block HEME >>> > in the file aminoacids.hdb (see the manual) >>> > >>> > >>> > Have anybody such missing parameters? >>> > >>> > >>> There aren't missing parameters, per se. The parameters are all there in >>> the .rtp and other force field files. You just need to construct an .hdb >>> entry for HEM, as pdb2gmx says. See the manual, section 5.6.4. >>> >>> -Justin >>> >>> -- >>> >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) >>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists