Hi so i did <font face="Arial"><font size="3">
<p>Remove unnecessary lines (the box vectors from the KALP structure,
the header information from the DPPC structure) and update the second
line of the coordinate file (total number of atoms) accordingly. After i use the <br></p><p>cat KALP_newbox.gro dppc128_whole.gro > system.gro <br><font face="Arial"><font size="3"><pre><br>when i check the file system.gro it has the protein and the lipid coordinates, however when i load to vmd to veiw , the VMD does not show anything , does any body have an idea what s wrong <br>
<br>Thank you <br><br></pre></font></font></p></font></font><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><font face="Arial"><font size="3"><pre>
<br><br></pre></font></font><div><div></div><div class="h5"><br><br><br><br><div class="gmail_quote">On Wed, Aug 17, 2011 at 4:19 PM, Sara baretller <span dir="ltr"><<a href="mailto:sarabiocomputation@gmail.com" target="_blank">sarabiocomputation@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">ok i did find the script <br><br>thank you <br><div><div></div><div><br><br><br><div class="gmail_quote">
On Wed, Aug 17, 2011 at 4:03 PM, Sara baretller <span dir="ltr"><<a href="mailto:sarabiocomputation@gmail.com" target="_blank">sarabiocomputation@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Thank you <br><br>yes i removed the Remove unnecessary lines ... i found the <a href="http://inflategro.pl/" target="_blank">inflategro.pl </a><br>
when i click on the rl <a href="http://inflategro.pl/" target="_blank">inflategro.pl</a> it gives me Firefox can't find the server at <a href="http://inflategro.pl" target="_blank">inflategro.pl</a>. <br><div><div></div>
<div>
<br><br><br><br><br><a href="http://inflategro.pl/" target="_blank"></a><div class="gmail_quote">On Wed, Aug 17, 2011 at 3:17 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
<br>
Sara baretller wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div>
I am doing the protein in lipid tutorial . <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin/<u></u>gmx-tutorials/membrane_<u></u>protein/02_topology.html</a><br>
<br></div>
Pack the lipids around the protein, i dont see where is the script perl <a href="http://inflategro.pl" target="_blank">inflategro.pl</a> <<a href="http://inflategro.pl" target="_blank">http://inflategro.pl</a>><div>
<br>
<br>
I googled It and did not find it. Can you please send me the script or tell me where I can find it<br>
<br>
<br>
</div></blockquote>
<br>
Then Google again :) If you search "Inflategro" it is the first result that comes up.<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Also I used the cat KALP_newbox.gro dppc128_whole.gro > system.gro<br>
<br>
so I checked the system.gro in vmd and did not load anything. I was able to vew the KALP_newbox.gro and the dppc128_whole.gro but not the system.gro<br>
<br>
do I have to organize the system.gro because I can see that the protein in numbered from 1 to … then the lipids start from 1 ….end .. will that cause a problem<br>
<br>
</blockquote>
<br></div>
Numbering is irrelevant. You probably didn't clean up the file as instructed in the tutorial:<br>
<br>
"Remove unnecessary lines (the box vectors from the KALP structure, the header information from the DPPC structure) and update the second line of the coordinate file (total number of atoms) accordingly."<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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 href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><div><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
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