<div>Last question:</div>
<div> </div>
<div>I would like to visualise my whole trjajectory looking at one of the ligands only which stacked to the loop of my protein. Which option of trjconv will be suitable to see whole trajectory of this ligand withoout any shifts on the screen so I will be able to produce a movie? I assume I need to use ndx file of this ligand.</div>
<div> </div>
<div>thank you in advance</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Mon, Oct 24, 2011 at 3:26 PM, Steven Neumann <span dir="ltr"><<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>Thank you both!!!</div>
<div> </div><font color="#888888">
<div>Steven<br><br></div></font>
<div>
<div></div>
<div class="h5">
<div class="gmail_quote">On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<p>Hi Steven,</p>
<p>Output can also be .pdb or .gro</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p>
<blockquote type="cite">
<div>On Oct 24, 2011 3:59 PM, "Steven Neumann" <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>> wrote:<br><br>
<div>Sorry guys but I do not get this...</div>
<div> </div>
<div> </div>
<div>I used:</div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt"></span> </div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt">1. First make your molecules whole if you want them whole </span></div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt"></span> </div>
<div>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">trjconv </span>-f md2.trr -s md2.tpr <span style="COLOR: #222222">-pbc whole -o md2whole.xtc (I have chosen my whole system for input and output)</span></font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">2. I do not need cluster anything</span></font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">3. </span></font></font><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"><font color="#000000">Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.</font></span></font></font></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">trjconv </span><font color="#000000">-f md2whole.xtc -s md2.tpr </font><span style="COLOR: #222222">-dump 0 -o md2wholeDUMP.xtc ???</span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">I did not obtain any coordinate file as output can be only trajectory (trr or xtc file)</span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">4. How to use this frame in:</span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222"></span> </p><span style="COLOR: #222222">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">trjconv </span><font color="#000000">-f md2wholeDUMP.xtc -s md2.tpr </font><span style="COLOR: #222222">-pbc nojump -o md2wholeDUMPnojump.xtc ?????</span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">Please, help!</span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222"></span> </p><font color="#888888">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">Steven</span></p></font></span></span></font></font>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p><br><br></div></div>
<p><font color="#500050">On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>> wrote: > > Hi, > > You don't n...</font></p>
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