g_sgangle will do this for you. You're lucky your rings are planar ;)<br><br>Oliver<br><br><div class="gmail_quote">On 17 May 2011 16:34, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</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;">1. Determine some mathematical calculation that you want to apply to some atoms.<br>
2. make a .ndx group that includes all of those atoms<br>
3. Run g_traj -ox to output the coordinates of those atoms<br>
4. Apply your mathematical calculation using awk.<br>
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Can anyone tell how to calculate the normal-normal angle between two<br>
stacking tyrosine residues as a function of time.<br><font color="#888888">
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