Ok, I got it. I&#39;m checking the pages and I think I&#39;m gonna make it. Kind of helps to have the hopes high :)<br><br>Another question though, maybe this is a bit out of the scope of MODELLER but:<br><br><pre>PRES DISU         -0.36 ! Patch for disulfides. Patch must be 1-CYS and 2-CYS.<br>

ATOM 1:CB  CT2    -0.10 !<br>ATOM 1:SG  SM     -0.08 !           2:SG--2:CB--<br>ATOM 2:SG  SM     -0.08 !          /<br>ATOM 2:CB  CT2    -0.10 ! -1:CB--1:SG<br></pre>So, I get the syntax but I fail to understand one thing. Is that number -0.36 the overall charge of the residue or something? Because in the CHARMM Struct.doc file it says:<br>

<br><pre>[ATOM  &lt;I&gt;&lt;atomname&gt;  &lt;parameter type&gt;   &lt;charge&gt; ]<br></pre>But it doesn&#39;t mention anything next to the PRES line. Is this a MODELLER specific thing? What happens if I leave it blank? Is there a way to generate this automatically? Or are these set values written down somewhere?<br>

<br>Sorry for all the questions, but I&#39;m trying to figure out how this works and not just copy paste things..<br><br clear="all">João [ .. ] Rodrigues<br><br>(Blog)   <a href="http://doeidoei.wordpress.com">http://doeidoei.wordpress.com</a><br>

(MSN)   <a href="mailto:always_asleep_@hotmail.com">always_asleep_@hotmail.com</a><br>(Skype) rodrigues.jglm<br>