Hi Nehme, I've did simulations on TRAIL, which also contains a zinc-finger domain, involving three cysteines and a chloride ion. But it's not so simple. Luckily the exact parameters seemed not that vital, as the zinc apparently functions to keep the three subunits together and was in any case not directly related to the properties we were interested in. Still, I spent some time parameterizing it. For that I did quite a search of the available literature. You'll find some references in our 2008 Proteins paper. One of the most striking things is the still unresolved issue of the protonation state of zinc finger domains. Especially in the acidic environment around DNA, this may become an issue. It is why I have stayed away from zinc-finger domains lately, as they'd cost me too much work properly parameterizing them, even though our lab is doing experimental work on them and it would be interesting to complement that with MD. That's also why I mentioned to be interested in such parameters. Not in what you can readily calculate with QM or what you can get from automatic topology builders or even from literature, including my own. That doesn't solve the issue of the protonation state or overall charge of the complex. I won't trust any report on zinc-finger domain MD, unless it is shown to properly reproduce experimental properties, including what can be determined in relation to the protonation state.
Cheers, Tsjerk On Wed, May 20, 2009 at 10:40 AM, Nehme El Hachem <n...@aub.edu.lb> wrote: > Hi Tsjerk, > > I thank you for your help. Indeed, I am very new to GROMACS ( I have a Linux > Red hat 9.0 and I do have some issues installing the software). > > If you are interested, please find a link: > http://www.epress.com/w3jbio/vol2/harris2/harris.htm > Molecular Dynamics Simulation Of The Estrogen Receptor Protein In Complex > With A Non-Consensus Estrogen Response Element DNA Sequence In A 10 Angstrom > Water Layer. > > I am trying to do some molecular dynamics on the oestrogen receptor DNA > binding domain (PDB code: 1HCQ). I have InsightII with Discover3 and CHARMm > but I am confused with the type of forcefield that I need. Furthermore, I > have to add counterions to neutralize the system, so it seems complicated. > I wanted to try GROMACS, because it has many forcfields (ex: ffAmber) for > modeling this type of system. > > I appreciate your help, > > Nehme. > > -- 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
