Simulated Annealing

500 simulated annealing (SA) trajectories were generated with the AA2A model based on 2RH1. One set was simulated with the disulfide bonds while the other set was simulated without the disulfide (DISU) bond. The set with DISU was run using a low (400K) and high (500K) heating temperature. The goal of SA is to see if any of the resulting structures are closer ( with smaller RMSD) to 3EML.

3EML essentially acts as the answer in the mock modeling trial. In order to see how the answer structure (3EML) behaves in SA, 500 SA runs were generated using a low (400K) and high (500K) heating temperature. Because the intracellular loop (ICL) between TM5 and TM6 is missing in 3EML, two 3EML structures were used. One structure had TM5 and TM6 connected on the intracellular side although the ICL is missing. The other structure had TM5 and TM6 separated (not connected) on the intracellular side.