Hi Nehme, > Also, in our zinc finger models, the zinc plays a structural role and it is > not implicated in DNA recognition. Furthermore, I will read your paper and > the references. I looked in the Literature and from NMR studies/X-ray and MD > done on zinc fingers containing a zinc ion coordinated to 4 cysteines. It > seems that these cysteines are deprotonated and the remaining negative > charges are stabilized by nearby positively charged side chains of arginines > or lysines.
It's hard, although not impossible, to assess the protonation state of such a center experimentally. Mind that crystal structures and NMR structures also use force fields and predefined topologies to model the structure. That means that you will only get out what you put in. If you set some group to be deprotonated while it should be protonated, this may be hard or even impossible to track down. You may still get a reasonable fit to the experimental data. For such issues Xray/NMR are not the best means. Note that I'm not saying you're wrong, but you should justify your choices. > I tried to use CHARMM forcefield, but every time I had the 4 cysteines > protonated, the coordination bonds removed and the parameters for zinc not > assigned. > How can I solve this issue? > In Gromacs you can use the file specbond.dat to define special bonds. Have a look at http://wiki.gromacs.org/index.php/specbond.dat and search the archives for more information. Cheers, Tsjerk -- 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
