Hi, Justin raises a number of problems, but there's another one. Copper is a transition metal with a specific coordination which depends on the oxidation state. If you only use bonds, you sort of assume that the coordination geometry is the result of a size-exclusion effect. In this respect, copper is to be regarded an exotic species:
http://wiki.gromacs.org/index.php/Exotic_Species Cheers, Tsjerk On Sat, Mar 21, 2009 at 1:05 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > DimitryASuplatov wrote: >> >> Hello, >> I am working with enzyme that contains Cu2+ in the active site. During a >> free simulation it always gets out due to minor conformational changes >> of coordinating residues. Since the copper is known to be essential for >> enzyme catalysis I want to set some extra force to bind it to certain >> residues. >> >> 1/ I have not found CU2+ in opls ff. In ions.itp CU is defined as CU2+ >> atomtype which I think is taken from GMX ff. Is it correct to use GMX >> Copper parametrization with OPLS? >> > > If you are ever asking yourself, "Can I take part of one force field and > introduce it into another?" the answer is always *absolutely not.* > > However, CU2+ is part of OPLS (in ions.itp, there is CU2+ after #ifdef > _FF_OPLS), and a reference for these parameters is given in ffoplsaa.atp. > >> 2/ What is the easiest way to bind a metal ion to a histidine residue? >> What if I add the bond to specbonds.dat without changing HIS topology >> (dihedral can be set to 0 0 0 0 0 0 in the itp file of the protein)? Can >> this be correct? >> > > You can try it and see. Whether or not you think it's appropriate is going > to depend on what is known about your particular system. But if you are > defining a bonded interaction of any sort between a metal ion and an amino > acid side chain, I would argue that the original HIS topology is no longer > valid, since it is sharing electrons with the metal, thus affecting the > charge of all species involved in the bonded interaction. > > -Justin > >> Thanks. I appreciate your time. >> SDA >> >> _______________________________________________ >> gmx-users mailing list gmx-us...@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-us...@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php