<div dir="ltr">Thank you both! Omer.<br clear="all"><br>Koby Levy research group,<br>Weizmann Institute of Science. <br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
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<div class="gmail_quote">On Sat, Sep 13, 2008 at 15:57, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d"><br><br>Omer Markovitch wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hello,<br>I would like to ask for your help in defining groups:<br>Say I have a protein. I would like to have two groups (1) the Calpha backbone (2) everything else.<br>
Later on, I will want to freeze the Calpha group.<br>How can I define these groups? Where?<br>I have looked in the manual, but I do not understand how to do it and in which files.<br></blockquote><br></div>Groups are defined in index files (.ndx), which are created with make_ndx. Calpha is a default group read in from a protein structure. To create a group that is everything but Calpha (group 3 in the make_ndx list), you would use<br>
<br>!3<br><br>at the make_ndx prompt.<br><br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">Thank you, Omer Markovitch.<br><br>Koby Levy research group,<br>Weizmann Institute of Science.<br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/" target="_blank">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
<br><br></div>
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</div></blockquote><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
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