Protool/Yasara_interface.py
def shortMD(self,pdblines):
        """Do a short MD in vacou to get an ensemble"""
        objs=self.Y.BuildPDB(pdblines)
        self.Y.DelRes('WAT')
        self.Y.DelRes('HOH')
        self.Y.Clean()
        self.Y.CellAuto(extension=10)
        self.Y.ForceField('Amber99')
        self.Y.Boundary('Periodic')
        self.Y.TempCtrl('SteepDes')
        self.Y.Sim('On')
        self.Y.Wait('SpeedMax<1000')
        self.Y.Sim('Off')
        self.Y.TempCtrl('Rescale')
        self.Y.Sim('On')
        raw_input('yes?')
        return
        #self.Y.Temp(298.15,'Yes')
Do a short MD in vacou to get an ensemble
Do a short MD in vacou to get an ensemble
Do a short MD in vacou to get an ensemble
def shortMD(self,pdblines):
        objs=self.Y.BuildPDB(pdblines)
        self.Y.DelRes('WAT')
        self.Y.DelRes('HOH')
        self.Y.Clean()
        self.Y.CellAuto(extension=10)
        self.Y.ForceField('Amber99')
        self.Y.Boundary('Periodic')
        self.Y.TempCtrl('SteepDes')
        self.Y.Sim('On')
        self.Y.Wait('SpeedMax<1000')
        self.Y.Sim('Off')
        self.Y.TempCtrl('Rescale')
        self.Y.Sim('On')
        raw_input('yes?')
        return
def shortMD ( self , pdblines ) : objs = self . Y . BuildPDB ( pdblines ) self . Y . DelRes ( 'WAT' ) self . Y . DelRes ( 'HOH' ) self . Y . Clean ( ) self . Y . CellAuto ( extension = 10 ) self . Y . ForceField ( 'Amber99' ) self . Y . Boundary ( 'Periodic' ) self . Y . TempCtrl ( 'SteepDes' ) self . Y . Sim ( 'On' ) self . Y . Wait ( 'SpeedMax<1000' ) self . Y . Sim ( 'Off' ) self . Y . TempCtrl ( 'Rescale' ) self . Y . Sim ( 'On' ) raw_input ( 'yes?' ) return
Do a short MD in vacou to get an ensemble
Do a short MD in vacou to get an ensemble
"""Do a short MD in vacou to get an ensemble""" #self.Y.Temp(298.15,'Yes')
self
pdblines