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

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