Hi, Ben,
I am using the flexEM package in modeller to refine a large complex. However, it took a long time for one CG/MD cycle. I wonder can I run the job in parallel ?
Maybe you can directly edit the script below.
Thanks!
Rui
# ============================================================================ # # a. Define the type of oprimization: conjugate gradients minimization (CG) # or molecular dynamics (MD) # b. Edit input parameters: density map parameters and probe structure # # ======================= Maya Topf, 4 Dec 2007 =============================
from modeller import * import shutil import sys, os, os.path import string import math from CG import opt_cg from MD import opt_md
env = environ()
############### INPUT PARAMETERS ################## optimization = 'MD' # type of optimization: CG / MD rigid_filename = 'rigid.txt' # rigid bodies file name path = './' # directory path code = '1ake' # 4 letter code of the structure input_pdb_file = '1ake_init.pdb' # input model for optimization em_map_file = '1ake_10A.mrc' # name of EM density map (mrc) format='MRC' # map format: MRC or XPLOR apix=1.0 # voxel size: A/pixel box_size=69 # size of the density map (cubic) resolution=10.0 # resolution x=-9.0; y=14.0; z=-8.0 # origin of the map num_of_runs = 1 # number of runs initial_dir = 1
############### RUN OPTIMIZATION ################## # CG # ---- if optimization == 'CG': for i in range(initial_dir,initial_dir+num_of_runs): scratch = path + '/' + str(i) + '/' os.system("mkdir -p " + scratch) os.system("cp " + path + '/'+ input_pdb_file + " " + scratch) os.chdir(scratch) opt_cg(path, code, str(i), 55*i, em_map_file, input_pdb_file, format, apix, box_size, resolution, x, y, z, rigid_filename)
# MD # ---- elif optimization == 'MD': for i in range(initial_dir,initial_dir+num_of_runs): scratch = path + '/' + str(i) + '/' # input_pdb_file = 'final' + str(i) + '_cg.pdb' # os.chdir(scratch) opt_md(path, code, str(i), 10*i, em_map_file, input_pdb_file, format, apix, box_size, resolution, x, y, z, rigid_filename)