Thanks for your last reply, now the script (concerning the symmetry models)
works well but after a few minutes the calculation ends with the following
message on the log file:
<< end of ENERGY.
runcmd______> restraints.make((def)residue_span_range=(0, 99999),
(def)residue_grouping=1, restraint_type='stereo',
(def)restraint_sel_atoms=1, (def)restraint_group=26,
(def)basis_pdf_weight='LOCAL', (def)distance_rsr_model=1,
(def)maximal_distance=999.0,
(def)basis_relative_weight=0.050000000000000003, spline_on_site=False,
(def)residue_span_sign=True, (def)intersegment=True, add_restraints=True,
(def)dih_lib_only=False, (def)spline_dx=0.5, (def)spline_min_points=5,
(def)spline_range=4.0, (def)mnch_lib=1, (def)accessibility_type=8,
(def)restraint_stdev=(0.0, 1.0), (def)restraint_stdev2=(0.0, 0.0, 0.0),
(def)sheet_h_bonds=7, (def)surftyp=1, (def)restraint_parameters=(3, 1, 3, 3,
4, 2, 0, 0.0, 0.086999999999999994), (def)distance_atoms=('CA', 'CA'),
(def)atom_ids=('',), (def)residue_ids='')
make_re_417_> Restraint type to be calculated: stereo
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 1810
2472 2851 788
Total number of restraints before, now : 0
7921
make_re_422_> Number of previous, current restraints : 0
7921
make_re_423_> Number of previous, current selected restraints: 0
7921
runcmd______> model.randomize_xyz(deviation=3.0)
randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1757 1757
1 3.0000
randomi_496_> Amplitude is > 0; randomization is done.
runcmd______> model.optimize(optimization_method=1,
(def)init_velocities=True, (def)temperature=293.0, (def)md_time_step=4.0,
(def)min_atom_shift=0.01, (def)cap_atom_shift=0.20000000000000001,
(def)write_all_atoms=True, (def)no_ter=False, (def)trace_output=0,
(def)equilibrate=999999, max_iterations=300, (def)residue_span_range=(0,
99999), md_return='FINAL', output='REPORT', (def)id2=1,
(def)root_name='undf', (def)file_id='default', (def)file_ext='',
(def)output_directory='')
pair2___215E> Dynamic memory allocation failed.
Routine, variable, status: icat1
Mod8v2 generates the:
.ini
define_symmetry-1.atm
define_symmetry-2.atm
.pdb
files.
When mod8v2 was released I used it but the result does not changed. Where is
the trouble?
I attached here my new2.py.
I'm building a model of a homopentamer with 1055 amino acids, is it too big
for the software requirements?
Thanks in advance.
Giovanni
****************************************************
Dr. Giovanni GRAZIOSO
Istituto di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42 - 20131 Milano (Italy)
Phone: 02/50317570 Fax: 02/50317565
e-mail:
Web site: http://users.unimi.it/demicheli/gg1.htm
****************************************************
Attachment:
new2.py
Description: Binary data