Hi Diana Bredenberg and Nilsson Int journal of Quantum Chem 83, 230-244 2001 This paper describes modeling of Zinc Sulfhydryl bonds in Zinc fingers The zinc is tetrahedrally coordinated.
Hope it helps. Alpay Date: Fri, 09 Jun 2006 15:51:03 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: [gmx-users] Re: Parameters for metals bonds inside proteins To: [EMAIL PROTECTED], Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Diana Rodriguez Ortiz wrote: > Hi, > > I thank you for your attention. I tried to use the mailing list but something has changed in that web page and I > did not figure out how to enter my query. The metal is Zn and it is in a tetrahedral strucuture. It is not completely > shielded from the environment. > > Thanks, > Diana > > > David van der Spoel <[EMAIL PROTECTED]> wrote: > Diana Rodriguez Ortiz wrote: > >> Hi Mr. Spoel, >> >> I am working with a small protein (50 aminoacids) that has a metal atom near its center. Where can I find the >>parameters to be able to run a molecular dynamics of this protein? In this one, the metal is tied to 4 sulfurs I will >>run it with gromacs. Can you help me? >> > > This is not simple, you will have to search the literature and/or > perform quantum calculations to obtain charges. You do not give much > details though. What metal? Is it tetrahedrally coordinated, i.e. is the > metal shielded from the environment completely? In that case you can > make chemical bonds using the specbond method. > > Please continue this discussion on the gromacs mailing list. > > >>Cordiially, >>Diana Rodriguez >>Intern at RPI >> >>------------------------------------------------------------- >> Antes ahora y siempre COLEGIO >> University of Puerto Rico at Mayaguez >> http://www.uprm.edu >>------------------------------------------------------------- >> > > > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php