<div>Hi Justin,</div>
<div>Thank you very much. I did not know that...<br></div>
<div class="gmail_quote">On Thu, Aug 13, 2009 at 8:42 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="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Jamie Seyed wrote:<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">my command is:<br>genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol 1 -ci insert.gro<br>
I also tried<br>genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol 1 -ci insert.gro -try 100<br>by using 20,30,40...,100 but each time was the same. (I also did it without shell command but no success)<br>
</blockquote><br></div>You can't run -cs and -ci at the same time; they must be done in separate processes. I would also get rid of -shell, in any case. If you're filling the box with water, adding an additional shell of solvent has no effect.<br>
<font color="#888888"><br>-Justin</font>
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<div class="h5"><br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<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>========================================<br>_______________________________________________<br>
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