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Despite its better use of memory, it seems that "array too small"
occurs in 8v0 also. I used the following top file and a pdb file
containing 70 residues and 2 calciums. After calculating the 5 loop
models, it read in the models for clustering. Then it started to do the
clustering, with the following log file (I've just included the part
pertaining to the clustering. The optimizing of the loops went OK). As
you can see, MBNDPF needed to be increased. I tried SET MAXRES = 5000,
which isn't supported any more, and SET TOPOLOGY_MODEL = 1, which
didn't change anything. What can be done? top file INCLUDE # include the standard routines # SET OUTPUT_CONTROL = 1 1 1 1 1 SET LOOP_MD_LEVEL = 'refine_3' #'nothing''refine_1'(fast)'refine_2''refine_3''refine_4''refine_5(very slow); SET TOPOLOGY_MODEL = 1 SET HETATM_IO = ON SET DYNAMIC_COULOMB = ON # SET SEQUENCE = 'LobeX' # the sequence code SET LOOP_MODEL = 'LobeX.pdb' # the structure into which the loop is built # SET LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 5 # how many loop models are calculated SET RAND_SEED = -34871 # to get different starting models each time SET ID2 = 0 CALL ROUTINE = 'loop' # do the loop models # # Try to get an even better model by clustering (optional): SET MODEL = 'LobeX.BL00010000' # one PDB structure SET EXPAND_CONTROL = LOOP_STARTING_MODEL LOOP_ENDING_MODEL 0 0 0 CALL ROUTINE = 'cluster', ID1 = LOOP_STARTING_MODEL, ID2 = LOOP_ENDING_MODEL # SUBROUTINE ROUTINE = 'select_loop_atoms' # insertion: PICK_ATOMS SELECTION_SEGMENT = '65: ' '70: ', SELECTION_STATUS = 'initialize' RETURN END_SUBROUTINE log file fndatmi_285W> Number of residues <> number of atoms; atom code: 72 70 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 72 70 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 72 70 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 72 70 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 72 70 CA Dynamically allocated memory at amaxalignment [B,kB,MB]: 3288527 3211.452 3.136 Dynamically allocated memory at amaxstructure [B,kB,MB]: 3315743 3238.030 3.162 mkfrw___326W> No selected atoms for frw position: 71 mkfrw___326W> No selected atoms for frw position: 72 malign3_328_> Initial framework positions: 72 mkfrw___326W> No selected atoms for frw position: 71 mkfrw___326W> No selected atoms for frw position: 72 mkfrw___326W> No selected atoms for frw position: 71 mkfrw___326W> No selected atoms for frw position: 72 mkfrw___326W> No selected atoms for frw position: 71 mkfrw___326W> No selected atoms for frw position: 72 mkfrw___326W> No selected atoms for frw position: 71 mkfrw___326W> No selected atoms for frw position: 72 malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 1 4 0.0000 Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 6.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 3.0000 Numb of residues in framework : 72 TOP_________> 522 649 SET ADD_SEQUENCE = on TOP_________> 523 650 SEQUENCE_TO_ALI ATOM_FILES = ATOM_FILES 'cluster.opt', AL; IGN_CODES = ALIGN_CODES 'cluster' Dynamically allocated memory at amaxstructure [B,kB,MB]: 3329259 3251.229 3.175 TOP_________> 524 651 TRANSFER_XYZ transfe_505_> MODEL is an average of the largest cluster: 1.5000 openf5__224_> Open 14 UNKNOWN SEQUENTIAL nmemb.dat openf5__224_> Open 16 UNKNOWN SEQUENTIAL occupancy.dat trfxyz___> The largest cluster occupancy: Template -1, occupancy: 1 72 Template -1, occupancy: 2 68 Template -1, occupancy: 3 67 Template -1, occupancy: 4 69 Template -1, occupancy: 5 50 transfe_511_> Number of templates for coordinate transfer: 5 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 544 0 TOP_________> 525 652 WRITE_MODEL FILE = 'cluster.ini' openf5__224_> Open 14 UNKNOWN SEQUENTIAL cluster.ini wrpdb2__568_> Residues, atoms, selected atoms: 72 544 544 TOP_________> 526 653 READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib\/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL8v0}/modlib/models.lib TOP_________> 527 654 READ_PARAMETERS FILE = '$(LIB)/par.lib' openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib\/par.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v0}/modlib\/par.lib rdparf__223E> Internal error: array too small: MBNDPF current maximum, current need: 250 251 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 3329259 3251.229 3.175 Starting time : 2005/06/08 13:38:33.907 Closing time : 2005/06/08 13:40:03.719 Total CPU time [seconds] : 89.64 |