Justin
1) So if I understood correctly I can make parametrisation of my uncommon group by the atb for instance. Than I can change itp file to rtp form and integrate this new residue to the existing ff. Finally when I will run pdb2gmx on the protein with the same group (even with different atom order) I obtain proper topology.top file. Doest it correct ? 2) I've defined bond between both of my atoms as the gb_15 and define this atoms as the C in the topology.top. Than I've run minimisation and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form and were not in the planar form :( What else should I do ? Could some operations with the angle term in topology.top help me? I've modified 612 613 614 2 as the ga_27 but it also could not help me. James 2012/6/10 Justin A. Lemkul <jalem...@vt.edu> > > > On 6/10/12 8:03 AM, James Starlight wrote: > >> Justin, >> >> thanks again for help. >> >> Finally is there any generall solution to parametrise hetero-groups >> covalently >> bonded with the protein ? Many proteins consist of such groups e.g >> chromophore >> in GFP, retinall in rhodopsin as well as some prostetic groups in the >> enzymes. >> >> > Parameterization schemes differ across force fields. It's never easy. > > > I've tried to make something like you've told me via inclusion of >> pre-parametrised residues in the existing gromacs ff but forced with some >> problems due to the atom order in new ITP and gro files provided by ATb or >> PRODRG are different from initial pdb file so pdb2gmx on the whole >> protein where >> het-group in the old order would not work properly :( >> >> > The output .itp files of ATB or PRODRG are not what you should be using. > You can't #include a covalently attached residue and expect the resulting > dynamics to be relevant; it's not like a ligand. > > What you need to do in those cases is create an .rtp entry (and any other > incidental bonded and nonbonded additions, as stated before) that specifies > whatever parameters you believe to be reliable. At that point, when the > .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the > atoms it needs, it builds the topology. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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