does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug server and after checking the topology I found that it has deleted of the hydrogen.
On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bharat gupta wrote: > >> Hi Justin, >> >> I am having following doubts regarding umbrella sampling of phosphate ion >> binding to my protein . >> >> 1. As per the tutorial, I need to fix an immobile reference. In my case >> which region do I have to fix as my protein consists of one single chain. >> Since I am studying the binding and unbinding of ion, shall I fix the ion >> fixed. If it's so, then do I have to give a different chain name for it as >> my complex doesnot chain name for ion/ligand. >> >> > You don't need an immobile reference just because my tutorial did. I had a > particular need to do so. For your purpose, I highly doubt it's necessary. > You're looking at small molecule-protein interactions, not protein-protein > interactions. > > > 2. What should be the size of box and how do I know where to place the >> protein's COM in box (the precise location). >> >> > The absolute COM is somewhat irrelevant; all distances during pulling are > relative. You can place the protein in a certain location in the box for > convenience if you like. The box size must be greater than twice the pull > distance, as explained in the tutorial. The amount that you wish to pull > will dictate both the location of the protein and the box size. > > -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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