Hi Ram, The total energy of the system before minimization and at each update is reported in the Reply Log (under Favorites menu). However, the purpose of the minimization tool is to clean up bad local geometries (strains and clashes) -- the energy values are not useful for quantitative analyses. They are only potential energies, not free energies (they do not include full solvation effects, sampling, or entropies) and the minimization only goes toward a local minimum rather than finding a global minimum. Chimera does not do free energy calculations. You would need to use some other program for those more computationally intensive studies. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 29, 2009, at 8:26 AM, r n wrote:
hi I wanted to do energy minimization for the pdb file with two chains by keeping their backbone fixed , tried chimera energy minimization but did not give me any energy after the minization or binding energy for the complex.
Is it anyway that I could do simulation of side chains and obtain the energy values such as lowest minima or the binding energy for two chains, using chimera? thanks ram