Elaine, <br>I guess i can use either &#39;minimize&#39; or &quot;addh and addcharge&quot; otherwise it will run the antechamber twice. <b>minimize is working fine but i can not save the result in mol2 format using COMMAND option.&nbsp; I try wrtiemol2 but it is not accepting it as a command. save is also not saving in mol2 format. <br>
</b>Any help, thanks in advance.<br>s<br><b><br></b><br><div class="gmail_quote">On Wed, Feb 27, 2008 at 5:48 PM, Elaine Meng &lt;<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>&gt; wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Conrad,<br>
&nbsp;From looking at the documentation, sounds like you can&#39;t use the<br>
minimize command with any nondefault settings of Dock Prep, addh, and<br>
add charge. &nbsp;Is that correct?<br>
<br>
It would be nice if it could tell that you already added hydrogens<br>
and charges to your liking and skip those steps. &nbsp;However, since this<br>
is all done via Dock Prep, that may or may not be possible.<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br>
UCSF Computer Graphics Lab and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<a href="http://www.cgl.ucsf.edu/home/meng/index.html" target="_blank">http://www.cgl.ucsf.edu/home/meng/index.html</a><br>
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</blockquote></div><br>