<div>Dear All</div>
<div>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.</div>
<div>
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<tr style="HEIGHT: 15pt; mso-yfti-irow: 4">
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<tr style="HEIGHT: 15pt; mso-yfti-irow: 5">
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri">@ s5 legend "Turn"</font></span></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri">@ s6 legend "A-Helix"</font></span></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri">@ s7 legend "5-Helix"</font></span></p>
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<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri">@ s8 legend "3-Helix"</font></span></p>
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<tr style="HEIGHT: 15pt; mso-yfti-irow: 9">
<td style="BORDER-RIGHT: #ece9d8; PADDING-RIGHT: 5.4pt; BORDER-TOP: #ece9d8; PADDING-LEFT: 5.4pt; PADDING-BOTTOM: 0in; BORDER-LEFT: #ece9d8; WIDTH: 251.45pt; PADDING-TOP: 0in; BORDER-BOTTOM: #ece9d8; HEIGHT: 15pt; BACKGROUND-COLOR: transparent" valign="bottom" nowrap width="335" colspan="3">
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri"><span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>46<span style="mso-spacerun: yes"> </span>24<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>7<span style="mso-spacerun: yes"> </span>10<span style="mso-spacerun: yes"> </span>36<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>3</font></span></p>
</td></tr>
<tr style="HEIGHT: 15pt; mso-yfti-irow: 10">
<td style="BORDER-RIGHT: #ece9d8; PADDING-RIGHT: 5.4pt; BORDER-TOP: #ece9d8; PADDING-LEFT: 5.4pt; PADDING-BOTTOM: 0in; BORDER-LEFT: #ece9d8; WIDTH: 251.45pt; PADDING-TOP: 0in; BORDER-BOTTOM: #ece9d8; HEIGHT: 15pt; BACKGROUND-COLOR: transparent" valign="bottom" nowrap width="335" colspan="3">
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri"><span style="mso-spacerun: yes"> </span>10<span style="mso-spacerun: yes"> </span>39<span style="mso-spacerun: yes"> </span>26<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>15<span style="mso-spacerun: yes"> </span>4<span style="mso-spacerun: yes"> </span>35<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0</font></span></p>
</td></tr>
<tr style="HEIGHT: 15pt; mso-yfti-irow: 11">
<td style="BORDER-RIGHT: #ece9d8; PADDING-RIGHT: 5.4pt; BORDER-TOP: #ece9d8; PADDING-LEFT: 5.4pt; PADDING-BOTTOM: 0in; BORDER-LEFT: #ece9d8; WIDTH: 251.45pt; PADDING-TOP: 0in; BORDER-BOTTOM: #ece9d8; HEIGHT: 15pt; BACKGROUND-COLOR: transparent" valign="bottom" nowrap width="335" colspan="3">
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri"><span style="mso-spacerun: yes"> </span>20<span style="mso-spacerun: yes"> </span>37<span style="mso-spacerun: yes"> </span>29<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>11<span style="mso-spacerun: yes"> </span>4<span style="mso-spacerun: yes"> </span>33<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>3</font></span></p>
</td></tr>
<tr style="HEIGHT: 15pt; mso-yfti-irow: 12">
<td style="BORDER-RIGHT: #ece9d8; PADDING-RIGHT: 5.4pt; BORDER-TOP: #ece9d8; PADDING-LEFT: 5.4pt; PADDING-BOTTOM: 0in; BORDER-LEFT: #ece9d8; WIDTH: 251.45pt; PADDING-TOP: 0in; BORDER-BOTTOM: #ece9d8; HEIGHT: 15pt; BACKGROUND-COLOR: transparent" valign="bottom" nowrap width="335" colspan="3">
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri"><span style="mso-spacerun: yes"> </span>30<span style="mso-spacerun: yes"> </span>37<span style="mso-spacerun: yes"> </span>32<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>11<span style="mso-spacerun: yes"> </span>2<span style="mso-spacerun: yes"> </span>35<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0</font></span></p>
</td></tr>
<tr style="HEIGHT: 15pt; mso-yfti-irow: 13">
<td style="BORDER-RIGHT: #ece9d8; PADDING-RIGHT: 5.4pt; BORDER-TOP: #ece9d8; PADDING-LEFT: 5.4pt; PADDING-BOTTOM: 0in; BORDER-LEFT: #ece9d8; WIDTH: 251.45pt; PADDING-TOP: 0in; BORDER-BOTTOM: #ece9d8; HEIGHT: 15pt; BACKGROUND-COLOR: transparent" valign="bottom" nowrap width="335" colspan="3">
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri"><span style="mso-spacerun: yes"> </span>40<span style="mso-spacerun: yes"> </span>36<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>31<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>10<span style="mso-spacerun: yes"> </span>6<span style="mso-spacerun: yes"> </span>30<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>3</font></span></p>
</td></tr>
<tr style="HEIGHT: 15pt; mso-yfti-irow: 14; mso-yfti-lastrow: yes">
<td style="BORDER-RIGHT: #ece9d8; PADDING-RIGHT: 5.4pt; BORDER-TOP: #ece9d8; PADDING-LEFT: 5.4pt; PADDING-BOTTOM: 0in; BORDER-LEFT: #ece9d8; WIDTH: 251.45pt; PADDING-TOP: 0in; BORDER-BOTTOM: #ece9d8; HEIGHT: 15pt; BACKGROUND-COLOR: transparent" valign="bottom" nowrap width="335" colspan="3">
<p class="MsoNormal" style="MARGIN: 0in 0in 0pt; LINE-HEIGHT: normal"><span style="COLOR: black; mso-ascii-font-family: Calibri; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: Calibri; mso-bidi-font-family: 'Times New Roman'"><font face="Calibri"><span style="mso-spacerun: yes"> </span>50<span style="mso-spacerun: yes"> </span>41<span style="mso-spacerun: yes"> </span>30<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>9<span style="mso-spacerun: yes"> </span>10<span style="mso-spacerun: yes"> </span>31<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>0</font></span></p>
</td></tr></tbody></table></div>
<div>Please suggest why I am not getting the actual number of residue in dssp file.</div>
<div>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</div>
<div>shahid nayeem </div>