[AMBER] Using WHAM to get 3D free energy surface in AMBER12

From: Wang Moye <wangmoye13.mails.ucas.ac.cn>
Date: Mon, 16 Mar 2015 15:30:40 +0800 (GMT+08:00)

Hello everyone!
I am a new user.There is a question in my objection and I need your help. I run a REMD process in AMBER12.Now I obtain some output files.Like this:
and remd.mdinfo.001.. remd.mdinfo.026
and remd.rst.001.. remd.rst.002
and remd.mdout.001.. remd.mdout.026
Total 26 replicas. I want to get the 3D free energy surface picture about my protein. Two coordinates are respectively Rg and RMSD.
Someone told me the WHAM code can do this. I have the WHAM code now, but I don't know how to use the WHAM to deal with my AMBER's output files to obtain the metafile. Should I write the Rg and RMSD information into a single metafile? How to achieve this using the outputfile above? Need I write some scripts to get the value of Rg and RMSD?
If you know how to deal with it, please help me. Thank you very much!

Wang moye
University of Chinese Academy of Sciences
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Received on Mon Mar 16 2015 - 01:00:02 PDT
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