Hi, I'm running a structure calculation for my protein using a simulated annealing protocol called refine_rama.inp which is similar to the /PROT_REFI/sa_dipo_coup_shift.inp protocol available in the xplor-nih- 2.9.6 version, apart from the use of Verlet dynamics. I'm using experimental restraints derived from NOEs, backbone dihedral angles, hydrogen bonds, CA and CB chemical shifts and RDCs together with Da and R values estimated from the distribution of dipolar couplings. When I run the structure calculation using the above mentioned restraints and only NH dipolar couplings I observe a peculiar behaviour during the high T dynamics steps which should be performed at 2000 K, that is the temperature increases rapidly during the dynamics up to 9473 K and then it slowly goes down again down to 2000 K where it stays for the second half of the high T dynamics. The cooling steps are performed correctly as far as temperature is concerned (finalT=100 K), and the final Energies obtained for 30 structures calculated are in the range 1083-4111 kcal/mol. When I add to the experimental data the dipolar couplings measured for NC' vectors, normalized respect to DNH, I observe the same increase in temperature during the high T dynamics, and even worse, a sudden increase in T up to 80292 K at the final stages of the cooling step (I_COOL=123 in the first structure) which compromises the results, in fact the output 30 structures have Energies in the range 8237-114391. Why are these sudden increase in T observed even if the tcoupling option is set to true? Are the Energy values of the first run (DNH only) reasonable? I'll be very happy to send as attached files the Xplor outputs. Thank you very much for yor help.
Giuliana
