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