AMBER Archive (2009)
Subject: [AMBER] The hydrophobic contribution
From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
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.