argument 1 complexes_prometcs read file complexes_prometcs argument 2 -format_cluster filename complexes_prometcs Entry init_record Ascii file detected 155 complexes_prometcs read actual version nb_type from the header= 2 ========= Summary header version version0.2 version number 2 type calc sda_2proteins int type calc 1 int type record 2 nb protein 2 nb_types 2 bit_integer 3 bit_real 119 nb other real 3 opt_sum F box_info F indice conf 0 indice traj 1 cm 1 49.814000000000000 49.796999999999997 -1.7509999999999999 cm 2 38.878000000000000 34.234000000000002 0.76100000000000001 Value of bits for integer: 3 11 Size: 16 refer to : run number refer to : step number Value of bits for energy : 119 1110111 Size: 16 term : 1 electrostatic term : 2 desolvation term : 3 hydrophobic term : 5 lennardjones term : 6 image_charge term : 7 metal_desolvation cm 1 49.814000000000000 49.796999999999997 -1.7509999999999999 cm 2 38.878000000000000 34.234000000000002 0.76100000000000001 Number of records 2000 Entry format_cluster max size 2000 o_record nb_complexe 2000 filename: complexes_prometcs.comp_cluster Info: There are some additional energy terms in the input, Info: The clust format supports only 4 fields for the energy terms. The following rules will apply: Info: 1. Lennard-Jones(PrometCS) will be added to Soft-core LJ Info: 2. Image-charge will be added to Electrostatic energy Info: 3. Metal Desolvation will be added to Soft-core LJ delete array_protein delete record END /exports/scratch/git/sda_test/sda_flex/sda_flex-7.3.2/examples/aubs/run ('before clustering ', 2000) ('After clustering: ', 29) N step cl_ size energy cl_size with SDA 1 31425 14 -3.853e+01 1.194900e+04 2 61764 153 -3.893e+01 1.473110e+05 3 92876 209 -3.685e+01 4.008790e+05 4 32652 40 -3.482e+01 2.484400e+04 5 44245 3 -3.903e+01 6.070000e+02 6 30391 1 -3.654e+01 7.780000e+02 7 61842 21 -3.284e+01 2.363700e+04 8 26814 11 -3.209e+01 4.362000e+03 9 85882 788 -3.091e+01 7.252120e+05 10 9649 154 -2.891e+01 5.817200e+04 11 54918 66 -2.650e+01 1.531100e+05 12 10630 329 -2.607e+01 1.652990e+05 13 12420 15 -2.697e+01 4.092000e+03 14 14652 54 -2.577e+01 1.736500e+04 15 59983 57 -2.523e+01 2.093500e+04 16 33696 5 -2.574e+01 1.197000e+03 17 25749 1 -2.709e+01 3.790000e+02 18 59320 16 -2.423e+01 5.446000e+03 19 66016 1 -2.696e+01 8.000000e+01 20 48427 7 -2.493e+01 3.034000e+03 21 48253 2 -2.562e+01 1.750000e+02 22 8977 13 -2.452e+01 4.892000e+03 23 54445 9 -2.444e+01 3.655000e+03 24 29964 1 -2.541e+01 1.520000e+02 25 34291 5 -2.391e+01 2.045000e+03 26 11417 2 -2.466e+01 3.540000e+02 27 22756 1 -2.488e+01 7.670000e+02 28 16433 1 -2.382e+01 9.700000e+01 29 33250 1 -2.357e+01 3.630000e+02 Entry trajectory2dcd filename mycluster.comp_cluster Min.pdb sda_input=sda_prometcs.in create pdbs from the 7 first complexes prefix name Min.pdb Entry init_record Ascii file detected 155 mycluster.comp_cluster read actual version nb_type from the header= 2 ========= Summary header version version0.2 version number 2 type calc sda_2proteins int type calc 1 int type record 2 nb protein 2 nb_types 2 bit_integer 3 bit_real 15 nb other real 3 opt_sum T box_info F indice conf 0 indice traj 1 cm 1 0.0000000000000000 0.0000000000000000 0.0000000000000000 cm 2 0.0000000000000000 0.0000000000000000 0.0000000000000000 Value of bits for integer: 3 11 Size: 16 refer to : run number refer to : step number Value of bits for energy : 15 1111 Size: 16 term : 1 electrostatic term : 2 desolvation term : 3 hydrophobic term : 4 repulsive_lj nb_line 29 nb_protein 2 nb_record 29 bool_input true will overload other data Reading SDA input file: sda_prometcs.in sda type, first protein is not flexible, discard array 1 protein pdb filename: ../data_grid/p2.pqr Number of atoms in pdb : 1432 nb_prot_out 1 tab_prot nb_grids 1 iprot1, iprot2 1 1 nb_tot_atoms 1432 nb_loop 7