def get_U_invU(asu_rst7_file_name): rst7 = Rst7.open(asu_rst7_file_name) UCbox = rst7.box U, invU = raf.CompXfrm(UCbox) return U, invU, UCbox
#! /usr/bin/env python import sander from chemistry.amber.readparm import AmberParm, Rst7 import numpy as np pdb = '3stl' parm = AmberParm('4amber_%s.prmtop' % pdb) #topo rst = Rst7.open('4amber_%s.rst7' % pdb) #box sander.setup(parm, rst.coordinates, rst.box, sander.pme_input()) ene, frc = sander.energy_forces() print ene.tot print max(frc) import code code.interact(local=dict(globals(), **locals())) sander.cleanup()
def get_U_invU(asu_rst7_file_name): rst7 = Rst7.open(asu_rst7_file_name) UCbox = rst7.box U, invU = raf.CompXfrm(UCbox) return U, invU, UCbox
#! /usr/bin/env python import sander from chemistry.amber.readparm import AmberParm, Rst7 import numpy as np pdb ='3stl' parm = AmberParm('4amber_%s.prmtop' %pdb) #topo rst = Rst7.open('4amber_%s.rst7' %pdb) #box sander.setup(parm, rst.coordinates, rst.box, sander.pme_input()) ene, frc = sander.energy_forces() print ene.tot print max(frc) import code; code.interact(local=dict(globals(), **locals())) sander.cleanup()
#! /usr/bin/env python import sander from chemistry.amber.readparm import AmberParm, Rst7 from chemistry.structure import Structure, read_PDB, write_PDB import numpy as np parm = AmberParm('4amber_1cby.prmtop') pdb = read_PDB('new.pdb') rst = Rst7.open('4amber_1cby.rst7') xyz = pdb.pdbxyz[0] sander.setup(parm,xyz, rst.box, sander.pme_input()) sander.set_positions(xyz) ene, frc = sander.energy_forces() #~ import code; code.interact(local=dict(globals(), **locals())) sander.cleanup()