Hi everyone,
I noticed that I have very high energies for my two docked proteins (using PRE as a restraint). I realized later that >99% of the high energies are from the crystal structure input. I determined the solution structure of the other protein, so I know what its energies are. Thus, I had been using these input structures (one with very high energies) for the docking script. How are others energy-minimizing a crystal structure? I had to add protons (in addition to CYSP/MTSL) to the crystal structure, so this may be the culprit. I tried a standard energy-minimization script (.inp) for NMR structures, but it didn't help. Any advice? Thanks, Valerie Villareal
