Thanks for your reply.. Actually I came across a paper "Molecular Modeling of the RNA binding N-terminal Part of Cowpea Chlorotic Mottle Virus coat Protein in Solution with Phosphate ion"... This paper was published in 1996, by Dr. David van der Spoel.. In this paper , they were trying to find out where exactly the phosphate ions bind to the peptide.
I thought may be I can try this but in their case it was a peptide and I am dealing with a barrel protein. As u said that I can go for docking and binding site prediction tools.. Since I am having some of docked complexes of my protein with phosphate ion, can I use MD for checking how strong the binding is or does the ion tries to move inside the barrel. On Mon, May 30, 2011 at 4:19 PM, Justin A. Lemkul <[email protected]> wrote: > > > bharat gupta wrote: > >> >> Hi, >> >> I want to dock a barrel protein with phosphate ion , to look for the sites >> where Phosphate ion binds... I searched the gmx list but I didn't find much >> related threads.. >> > > You usually won't find instructions specifically tailored for your > specialty application. This list is for general Gromacs usage. > Occasionally you'll find a how-to for something, but that's a rare find. > > > I want to do the following things... >> 1) Simulate the binding of phosphate ion with a barrel protein. Here I do >> not know where does the ions binds and thats what I want to find through >> simulation.. >> 2) After getting the site , I want to look for the binding affinities >> between the predicted sites.. >> >> I want to know how shall I approach this.. since I don't know how many >> ions I have to simulate with the protein..Can anybody help or refer to some >> paper?? >> >> > It sounds like you need to be looking at docking and/or binding site > prediction algorithms, neither of which can be done with Gromacs. Running > MD and hoping your PO4 stick somewhere is a great way to waste time and > probably not learn anything :) There are several ways to calculate binding > free energies after you've determined plausible binding sites. > > -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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