Hi all I was wondering if some body has done simulating multiple copies of small lead like fragments in a solvated box .
I want to soak my proteins with multiple copies of diverse fragments along with water as iam interested in finding the hot spots in proteins that can be successfully employed for fragment based drug design. The approach is analogs to the MCSS approach developed by Prof Karplus and the recent SILCS approach by Prof Mackerell. The impediments which i theoretically fore see are 1) how to negate interactions terms between two fragments as two fragments may be competing for the same site. 2) How to create multiple topologies for multiple copies of the same fragment randomly placed all over the fragment 3) Iam also skeptical whether the fragments will be able to find their respective binding site in a nanosecond time scale when started De Novo contrary to the well settled proposition of docking and keeping the fragment in the active site. A look at this paper by DE Shaw " How Does a Drug Molecule Find Its Target Binding Site??" reveals the binding event to be captured on a mili second time second. Thanking you in advance for all thought provoking suggestions. Regards Vijayan.R On Sat, Jan 14, 2012 at 10:45 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Hovakim Grabski wrote: > >> Hi, >> Anyone know any ligand- ligand tutorial? >> > > If there is no receptor, then there is no ligand ;) > > > I've been trying to set up a taurine simulation with >> lysophosphatidylcholines (LPC) with no success. >> > > Without a description of what you've tried, what hasn't worked, etc then > there's not much anyone can suggest. If you've simply got two small > molecules you want to simulate together: > > 1. Obtain topologies for both species and construct a .top that calls a > force field and the small molecule topologies > 2. Set up the coordinate file such that the two species are arranged how > you'd like them in a single box (done with editconf) > 3. Solvate and proceed as you would any other simulated system > > -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> >
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