On Wed, Nov 2, 2011 at 2:06 PM, Alex <span dir="ltr"><<a href="mailto:alexbioinfo@yahoo.com" target="_blank">alexbioinfo@yahoo.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All<br>
<br>
I'd like to perfom a deuterium oerder parameters analysys in a system with DPPC<br>
+ Protein + Water<br>
I read that I've to make an index file that contains one group each for every<br>
carbon atom in the acyl-chain (starting<br>
with the carbonyl-carbon and going further down).<br>
Where can I get carbon atoms index in the acyl-chain to group them? Have I to<br>
open the DPPC in pdbviewer<br>
</blockquote><div>yes, that's a way to do it.<br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
I need as well to make two index files: for sn1 and sn2 chains of DPPC.<br></blockquote><div>yes, that is correct.<br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Have I to run g_order in both ndx files (sn1 and sn2)?<br></blockquote><div>yes, that is also correct. make sure to write two different output files (sn1.out and sn2.out)<br><br> <br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<br>
Thanks<br>
<span><font color="#888888"><br>
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