<div>Hi Justin</div>
<div>I choose group 5 main chain for dssp calculation</div>
<div>Shahid Nayeem<br><br> </div>
<div><span class="gmail_quote">On 5/24/10, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q"><br><br>shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear All<br>I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows.<br>
</blockquote><br></span>When prompted, what group did you choose for the analysis?<br><br>-Justin<span class="q"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>@ s0 legend "Structure"<br><br> <br><br>@ s1 legend "Coil"<br><br> <br>
<br>@ s2 legend "B-Sheet"<br><br> <br><br>@ s3 legend "B-Bridge"<br><br> <br><br>@ s4 legend "Bend"<br><br> <br><br>@ s5 legend "Turn"<br><br> <br>
<br>@ s6 legend "A-Helix"<br><br> <br><br>@ s7 legend "5-Helix"<br><br> <br><br>@ s8 legend "3-Helix"<br><br> <br><br> 0 46 24 0 0 7 10 36 0 3<br>
<br> 10 39 26 0 0 15 4 35 0 0<br><br> 20 37 29 0 0 11 4 33 0 3<br><br> 30 37 32 0 0 11 2 35 0 0<br><br> 40 36 31 0 0 10 6 30 0 3<br>
<br> 50 41 30 0 0 9 10 31 0 0<br><br>Please suggest why I am not getting the actual number of residue in dssp file.<br>When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file<br>
shahid nayeem <br></blockquote><br></span>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>
Blacksburg, VA<br>jalemkul[at]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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