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:
remd.mdcrd.001
remd.mdcrd.002
...remd.mdcrd.026
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
2015/3
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Received on Mon Mar 16 2015 - 01:00:02 PDT
