<br><br><div class="gmail_quote">On Tue, May 8, 2012 at 1:01 PM, rama david <span dir="ltr"><<a href="mailto:ramadavidgroup@gmail.com" target="_blank">ramadavidgroup@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br><div class="gmail_quote">On Tue, May 8, 2012 at 1:00 PM, rama david <span dir="ltr"><<a href="mailto:ramadavidgroup@gmail.com" target="_blank">ramadavidgroup@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Gromacs user,<br> I am doing the justin tutorial on lipid posted on link......<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html</a><br>
<br>I am following the tutorial very carefully ...<br>As mentioned in the tutorial I need to generate strong position restrained on <br>proteins heavy atoms to ensure that position of atom does not change during EM<br>(Energy Minimisation )<br>
My command line is as follow .....<br><br>genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000 <br><br><br><br>Reading structure file<br>Select group to position restrain<br>Group 0 ( System) has 138 elements<br>
Group 1 ( Protein) has 138 elements<br>Group 2 ( Protein-H) has 109 elements<br>Group 3 ( C-alpha) has 16 elements<br>Group 4 ( Backbone) has 48 elements<br>Group 5 ( MainChain) has 64 elements<br>
Group 6 ( MainChain+Cb) has 78 elements<br>Group 7 ( MainChain+H) has 81 elements<br>Group 8 ( SideChain) has 57 elements<br>Group 9 ( SideChain-H) has 45 elements<br>Select a group: <br>
<br><br><br>I am using Gromacs 4.5.4 <br><br>Generally position restrain is applied on backbone of protein <br>So I choose backbone (4)<br><br>Is it right or I have to choose the group protein(138 elements) to apply position restraine on all protein atoms....<br>
<br></blockquote></div></blockquote><div><br></div><div>As the tutorial suggest you can restrain the heavy atoms, but I usually restrain the entire protein during the InflateGro steps (EMs) and let the lipids minimize around it.</div>
<div><br></div><div>-Anirban</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br><br> All suggestions are welcome <br> thank you in advance<span><font color="#888888"><br><br><br>Rama David .<br><br>
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