<div>Hi</div>
<div>No i dont have any capping group</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">Hi Justin<br>I choose group 5 main chain for dssp calculation<br></blockquote><br></span>Do you have any capping groups (N-acetyl, C-amine, etc)?<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Shahid Nayeem
<div><span class="e" id="q_128cb35b241132f3_2"><br><br> On 5/24/10, *Justin A. Lemkul* <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> shahid nayeem wrote:<br><br> Dear All<br> I did 10ns simulation of three peptide residue solvated in<br> water. Each peptide residue is 26 residue long. In final .gro<br> file it is showing total 78 residue which is O.K. as 3x26=78.<br>
For inserting three similar peptide I used genconf command. when<br> I run dssp I get total residue as 80. The command for dssp is<br> do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the<br> output of dssp run is as follows.<br>
<br><br> When prompted, what group did you choose for the analysis?<br><br> -Justin<br><br><br> @ s0 legend "Structure"<br><br> <br> @ s1 legend "Coil"<br><br> <br>
@ s2 legend "B-Sheet"<br><br> <br> @ s3 legend "B-Bridge"<br><br> <br> @ s4 legend "Bend"<br><br> <br> @ s5 legend "Turn"<br>
<br> <br> @ s6 legend "A-Helix"<br><br> <br> @ s7 legend "5-Helix"<br><br> <br> @ s8 legend "3-Helix"<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<br> in dssp file.<br> When I follow the same procedure for full protein molecule<br> simulation I get the same number of residue in dssp output as<br>
well as final.gro file<br> shahid nayeem<br><br><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></span></div> jalemkul[at]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080<span class="q"><br>
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<div><span class="e" id="q_128cb35b241132f3_10"><br>-- <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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