Hi, Is there any way to get the averaged distributions of ions around the protein surface.
On Thu, Dec 1, 2011 at 9:47 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bharat gupta wrote: > >> Yes, the phosphate ion moves around the protein but I am not able to find >> out how many of them bind to my protein. How can that be done ?? >> >> > You'll have to set a definition for what you consider to be binding. Is a > transient contact "binding?" Does the interaction have to persist for some > length of time to be considered? In any case, you can print a list of > contacts that occur with g_dist -dist, or use more complex selection > criteria and generate dynamic indices with g_select (see the help text for > examples). > > -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
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