Hello all I'm a begginer in this topic, and started to calculate "a" structure of a peptide on non-aqueous solvents.
The idea beyond torsion potentials seem's to be very nice. Indeed, I have few information about angles sidechain restraints, and in fact around 30% of the total energy per generated structure comes from ANGLEs potential term. So I expect to improve this number using torsion potentials. I thought in starting to use the torsion potentials, though not sure if it's correct when working with other solvents than water. Reading the mailing list, there's an answer about wether we should use or not the angles database if the experiment was done in other solvents than the aqueous media: http://dcb.cit.nih.gov/pipermail/xplor-nih/2004-March/000161.html So it seems that for proteins it could be used. So my question is: Are the following rama related commands in the anneal.py the correct ones to use the Rama torsion angle database in my case? #Rama torsion angle database # protocol.initRamaDatabase() potList.append( XplorPot('RAMA') ) rampedParams.append( MultRamp(.002,1,"potList['RAMA'].setScale(VALUE)") ) I'm using the anneal.py script (eginput/gb1_rdc) as a template to my calculations, though not using rdc stuff. Commented all RAMA stuff in my first runs. Cheers, Leo
