Hi, If you know the structure of the zinc binding domain and assume that the zinc ion stays in place it may be all right to use the bonded representation.
Recent publications: @article{Lin2010, author = {Lin, F and Wang, R}, title = {Systematic Derivation of {AMBER} Force Field Parameters Applicable to Zinc-Containing Systems}, journal = {J Chem Theory Comput}, volume = {6}, pages = {1852-1870}, year = {2010} } @Article{Peters2010, author = "Peters, M B and Yang, Y and Wang, B and F{\"u}sti-Moln{\'a}r, L and Weaver, M N and Merz, K M", title = {Structural Survey of Zinc Containing Proteins and the Development of the Zinc {AMBER} Force Field ({ZAFF})}, journal = "J Chem Theory Comput", year = "2010", volume = "6", pages = "2935-2947" } You have to know quite a lot on the structure to use this approach. Good luck, Ran. ------------------------------------------------ Ran Friedman BitrÀdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden NorrgÄrd, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/ccbg ------------------------------------------------ Message: 6 Date: Thu, 17 Feb 2011 23:46:02 -0800 From: bharat gupta <bharat.85.m...@gmail.com> Subject: Re: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users <gmx-users@gromacs.org>, baa...@smplinux.de Message-ID: <AANLkTi=7rJZLS6B+hQvjNH5Su=qf3y9ay75ebm9fh...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Thanks for these two references ... I am trying to simulate a zinc ion (Zn++) binding domains .. Actually the study involves grafting the Zinc ion domain onto some other protein to check whether it binds to ions or not and what will be the effect of ion binding onto the topology of the other protein to which the zinc ion binding domain is attached ..... On Thu, Feb 17, 2011 at 11:15 PM, Marc Baaden <baa...@smplinux.de> wrote: > > Hi, > > As mentioned by others, there's really lots of literature out there. I > thought I mention a recent study we carried out, because it actually > helped discover some new ion binding sites based on MD. By re-examining > crystal structures based on these results, we could even find > experimental evidence for those ions being there. [1] > > But actually you didn't tell us which ions you want to simulate? > Monovalent ions should be sort of ok, although there are differences > among the forcefields (some original KCl used to crystallize). > Di-valent ions, in particular Ca2+, are much more tricky. Higher > charged ones are a nightmare. The higher the charge, the more likely > you might want things like polarization in your simulation. > > There are also some specific forcefields finely parameterized for ions > based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh > and Piquemal. > > Good luck, > Marc > > [1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis > > http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000 > > [2] SIBFA (Sum of Interactions Between Fragments Ab initio computed) > http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html > > > bharat.85.m...@gmail.com said: > >> Thankx for the reply ... > >> Can you refer some papers which can be helpful for me to do MD > >> simulation of proteins with ions ... It will be of great help.. I > >> searched the gromacs user list but couldn't get much material.. > > > > -- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110217/caf3dcc7/attachment-0001.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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