On Tue, Feb 16, 2010 at 11:12 AM, sukesh chandra gain <suk...@atc.tcs.com>wrote:
> Dear All, > > It is not clear from manual how to analyse my requirements after > simulation. > Could you please help me in the following regards: > Please have a look at the g_ tools. http://www.gromacs.org/Documentation/Gromacs_Utilities make a proper index file according to your needs using make_ndx or you can do it manually also. Have a look at Gromacs manual. Chapter 8. > 1> How to get the graph on "occupancy of hydrogen bond interactions of > ligands throughout 5 ns simulation" and "occupancy of a particular > salt-bridge throughout the simulation" ? try g_hbond, g_saltbr depending on your system... you may look at other g_tools. > 2> I want to get a graph of the distances of some particular co-factor > atoms and active site residues atoms throughout the simulation. > Suppose I want the distance graph between DPM:C9B and Arg7:CA for total > simulation. > > g_dist > 3> Average hydrogen bond distance between active site residues and ligand. > > g_hbond > 4> RMSD of some particular residues from its initial structure. > g_rms, g_rmsdist > > 5> Total formal charge residing at active site throughout the simulation > (All +vely charge and -vely charge residues within 15 A radius of active > site will be considered). > > g_saltbr after converting trajectory with trjorder. > It would be a great help if you could kindly give some sample commands for > these analysis. > > Sorry for lots of questions. > > Thank You. > > Regards, > Sukesh > > > -- > Sukesh Chandra Gain > TCS Innovation Labs > Tata Consultancy Services Ltd. > 'Deccan Park', Madhapur > Hyderabad 500081 > Phone: +91 40 6667 3572 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > Cheers, Saikat ------------------------------------------------------------------- Saikat Banerjee Integrated Ph.D student Prof B. Bagchi's group Room no. 210 Solid State and Structural Chemistry Unit (SSCU) Indian Institute of Science Bangalore-560012 -------------------------------------------------------------------
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