<div dir="ltr">Jing-Yuan<div><br></div><div>When you ran the </div><div><br></div><div><pre class="" style="margin-left:2em;margin-right:2em;color:rgb(0,0,0)">phenix.build_amber_interface
</pre></div><div><br></div><div class="gmail_extra"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">did that run OK? Please send me the output.</div><div dir="ltr"><br></div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Apr 1, 2016 at 10:50 AM, Liu, Jing-Yuan <span dir="ltr"><<a href="mailto:jliu2@iu.edu" target="_blank">jliu2@iu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p><font size="2"><span style="font-size:10pt">Dear PHENIX Developers,</span></font></p>
<p><font size="2"><span style="font-size:10pt">I would like to perform phenix.refine using amber gradient. I installed AmberTools 15 and the newest version of Phenix by following the instruction found here
</span></font></p>
<p><font size="2"><span style="font-size:10pt"><a href="http://www.phenix-online.org/documentation/reference/amber.html" target="_blank">http://www.phenix-online.org/documentation/reference/amber.html.</a></span></font></p>
<p><font size="2"><span style="font-size:10pt">However, when I ran"phenix.AmberPrep", it complains "phenix.AmberPrep not found". In dead, I cannot find any binary named "phenix.AmberPrep". However, it looks to me that phenix is installed OK and so does AmberTools
15. I checked each step of my installation, I could not find anywhere is wrong. Can you please help me out? Thank you!</span></font></p>
<p><br>
<font size="2"><span style="font-size:10pt"></span></font></p>
<p><font size="2"><span style="font-size:10pt">Sincerely,<br>
Jing-Yuan</span></font><br>
</p>
</div>
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