<br><br><div class="gmail_quote">On Tue, Feb 16, 2010 at 11:12 AM, sukesh chandra gain <span dir="ltr"><<a href="mailto:sukesh@atc.tcs.com">sukesh@atc.tcs.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All,<br>
<br>
It is not clear from manual how to analyse my requirements after simulation.<br>
Could you please help me in the following regards:<br></blockquote><div><br>Please have a look at the g_ tools. <br><a href="http://www.gromacs.org/Documentation/Gromacs_Utilities">http://www.gromacs.org/Documentation/Gromacs_Utilities</a><br>
<br>make a proper index file according to your needs using make_ndx or you can do it manually also.<br><br>Have a look at Gromacs manual. Chapter 8.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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" ? </blockquote><div>
<br>try g_hbond, g_saltbr depending on your system... you may look at other g_tools.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
2> I want to get a graph of the distances of some particular co-factor atoms and active site residues atoms throughout the simulation.<br>
Suppose I want the distance graph between DPM:C9B and Arg7:CA for total simulation.<br>
<br></blockquote><div><br>g_dist<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
3> Average hydrogen bond distance between active site residues and ligand.<br>
<br></blockquote><div><br>g_hbond<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
4> RMSD of some particular residues from its initial structure.<br></blockquote><div><br>g_rms, g_rmsdist<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
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).<br>
<br></blockquote><div><br>g_saltbr after converting trajectory with trjorder.<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
It would be a great help if you could kindly give some sample commands for these analysis.<br>
<br>
Sorry for lots of questions.<br>
<br>
Thank You.<br>
<br>
Regards,<br>
Sukesh<br>
<br>
<br>
-- <br>
Sukesh Chandra Gain<br>
TCS Innovation Labs<br>
Tata Consultancy Services Ltd.<br>
'Deccan Park', Madhapur<br>
Hyderabad 500081<br>
Phone: +91 40 6667 3572<br><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>Cheers,<br><br>Saikat<br><br>-------------------------------------------------------------------<br>Saikat Banerjee<br>Integrated Ph.D student<br>Prof B. Bagchi's group<br>
Room no. 210<br>Solid State and Structural Chemistry Unit (SSCU)<br>Indian Institute of Science<br>Bangalore-560012<br>-------------------------------------------------------------------<br>