Well, mine is a beta-barrel protein called Green Fluorescent Protein. In such a case the movement of ion is very important. As the ion in side the barrel can quench the fluorescence. That's what I want to track..
On Mon, May 30, 2011 at 4:57 PM, Justin A. Lemkul <[email protected]> wrote: > > > bharat gupta wrote: > >> Thanks a lot.. If I am not wrong SMD and Umbrella sampling will help me in >> determining the binding affinity. So, my first objective can be achieved >> with it. >> >> Then what about the movement of ions into the barrel. Will it be possible >> to track it with MD coz the movement of ion is very important in my case. I >> don't want them to enter the barrel rather I want them to be on the surface >> of the barrel?? >> >> > You can implement such restraints, or guide the ion through the channel, > whichever you prefer. The literature is rich with studies of the movement > of ions and small molecules through transporters and channels. > > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 [email protected] > 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 [email protected]. > 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 : [email protected]
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