by the way also I've tried to make model of cytochrome p450 in charmm. In that case heme have only one coordinate bond with the side chain of cysteine (not 2 covalent bonds with cysteines as in the cytochrome-C). So as I understand I should include model of heme as the diffusion ligand ( as the separate itp file in the topology) should'n it ? How I can define coordinate bond of the heme's FE atom with the cysteine side chain (in the pdb2gmx I found that such can be done only for histidines)?
James 2013/4/12 Mark Abraham <mark.j.abra...@gmail.com> > Look in the literature... > > > On Thu, Apr 11, 2013 at 2:12 PM, James Starlight <jmsstarli...@gmail.com > >wrote: > > > During the past few days I've tried to make parametrization of any > > heme-containing cythochromes and always failed with the huge errors about > > missing parameters. Could someone provide me with such params (i suppose > it > > should be added to thebonded/non-bonded.itps of the force field besides > the > > rtps) for any ful-atomic force field? Finally I've not found in mailing > > list any possible sollution of the same problems. > > > > > > James > > > > 2013/4/4 James Starlight <jmsstarli...@gmail.com> > > > > > It was strange for me the big number of such errors :) > > > May the construction of new scheme for the hydrogens in the .hdb file > > > partly solve my problem ? ( as I've mentioned previously i had mismatch > > in > > > 2 hydrogens ( in comparison to the NMR-like structure). > > > Should also HEME be added in the residuetype.dat as the part of the > > > protein? > > > > > > Finally I'll be thankful to everyone who could provide me with the any > > > cytochrome properly parametrized in charmm :) > > > > > > James > > > > > > > > > 2013/4/3 Justin Lemkul <jalem...@vt.edu> > > > > > >> On Wed, Apr 3, 2013 at 10:27 AM, James Starlight < > > jmsstarli...@gmail.com > > >> >wrote: > > >> > > >> > 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 ? > > >> > > > >> > > > >> Heme is tricky, and this error comes up every time someone tries to > use > > >> heme in Gromacs (see the archive for tips and possible solutions). > > >> Parameters are missing for bonded interactions, so either add them > > >> directly to the .top or to ffbonded.itp. You'll have to search the > > >> literature for suitable parameters or derive them yourself. There are > > >> lots > > >> of reports of heme-containing proteins being simulated, so clearly the > > >> fully parameter set exists somewhere. > > >> > > >> -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 > > > -- > 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
