The code would not know that <i>a priori</i>. This list is generated before the frames are analyzed.<div><br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div> <br><br><div class="gmail_quote">On Tue, Jul 27, 2010 at 12:40 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div><div></div><div class="h5"><br>
<br>
Ilya Chorny wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have a question about the g_saltbr output. I looked through the mailing list and could not find a suitable answer. <br>
The initial output lists all the charge group i.e.<br>
<br>
CG: ARG24 Q: 0.07 Atoms: 58 59 60<br>
CG: ARG24 Q: 0.31 Atoms: 61 62 63<br>
CG: ARG24 Q: 0.38 Atoms: 64 65 66<br>
CG: ARG24 Q: 0.12 Atoms: 67 68 69<br>
CG: ARG24 Q: 0.12 Atoms: 70 71 72<br>
CG: ASP28 Q: -0.1 Atoms: 79 80 81<br>
CG: ASP28 Q: -0.9 Atoms: 82 83 84<br>
CG: ARG36 Q: 0.07 Atoms: 94 95 96<br>
CG: ARG39 Q: 0.31 Atoms: 97 98 99<br>
CG: ARG42 Q: 0.38 Atoms: 100 101 102<br>
CG: ARG45 Q: 0.12 Atoms: 103 104 105<br>
CG: ARG48 Q: 0.12 Atoms: 106 107 108<br>
CG: ARG60 Q: 0.07 Atoms: 118 119 120<br>
CG: ARG63 Q: 0.31 Atoms: 121 122 123<br>
<br>
In some cases it lists 4 charge groups for ARG (i.e. ARG24) and in others it list 1 charge group (i.e. ARG 36). Why is this?<br>
<br>
</blockquote>
<br></div></div>
Perhaps because not all the charge groups of Arg36 are participating in salt bridges, whereas in Arg24 they are.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks,<br>
<br>
Ilya<br>
<br>
<br>
<br>
-- <br>
Ilya Chorny Ph.D.<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Ilya Chorny Ph.D.<br><br>
</div>