AMBER Archive (2009)

Subject: [AMBER] The hydrophobic contribution

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Thu Oct 08 2009 - 00:48:32 CDT

Dear amber users,

Here I am really appreciated for your help all the time. Now, I still have a problem, the amber cannot be installed in the cluster of our institute but on my private computer. I want to calculate the binding free energy of my protein complex. I have used apbs to calculate the electrostatic contributions, and now I want to calculate the hydrophobic contributions, do anyone here, know how can I do this job, can amber do this? I just want calculate the binding energy from 10 frames for one complex, I have more than 40 complexes, I can hardly calculate them one by one by run long time MM/PBAS.
Thanks for your help!

Rilei Yu

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