similarly, why would CA-CB-CG-OD2/1 in ASP be gd_40 instead of gd_34 ?<br><br>
<p class="MsoPlainText"><span style="font-family:"Courier New"">#define
gd_34<span style="mso-spacerun:yes"> </span>0.000<span style="mso-spacerun:yes"> </span>5.92<span style="mso-spacerun:yes"> </span>3<br>
; -CHn,SI-CHn-<span style="mso-tab-count:1"> </span>1.4<br>
;<br>
</span></p>
...<br>
<p class="MsoPlainText"><span style="font-family:"Courier New"">#define
gd_40<span style="mso-spacerun:yes"> </span>0.000<span style="mso-spacerun:yes"> </span>1.0<span style="mso-spacerun:yes">
</span><span style="mso-spacerun:yes"> </span>6<br>
; -CHn-C,NR(ring), CR1-<span style="mso-tab-count:1"> </span>0.24<br>
;<br>
</span></p>
....<br><br>Something wrong with my interpretation of the comments after each definition?<br><br>Thanks,<br> <br>Yun Shi<br><div class="gmail_quote">On Wed, Aug 24, 2011 at 3:00 PM, Yun Shi <span dir="ltr"><<a href="mailto:yunshi09@gmail.com">yunshi09@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,<br><br>For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ?<br>
<br>In /gromos53a6.ff/ffbonded.itp, it appears:<br><br>
<p><span style="font-family:"Courier New"">#define
gd_29<span> </span>0.000<span> </span>3.77<span> </span>3<br>
; -C,CHn,SI-<span> </span>0.9<br>
;<br>
</span></p>
...<br>
<p><span style="font-family:"Courier New"">#define
gd_41<span> </span>0.000<span> </span>3.77<span> </span>6<br>
; -CHn-NT-<span> </span>0.9<br>
;<br>
</span></p>
...<br><br>Thanks,<br><font color="#888888"><br>Yun Shi<br>
</font></blockquote></div><br>