Jing-Yuan When you ran the phenix.build_amber_interface did that run OK? Please send me the output. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, Apr 1, 2016 at 10:50 AM, Liu, Jing-Yuan wrote:

Dear PHENIX Developers,

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

http://www.phenix-online.org/documentation/reference/amber.html. http://www.phenix-online.org/documentation/reference/amber.html

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!

Sincerely, Jing-Yuan

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