/home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4 n_dec 21 Sun Jul 26 18:05:02 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for na and prot molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.1 step is too small for the max.(64x64x64) grid\/home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4 /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4 /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4 /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4 /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4 n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for na and prot molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for na and prot molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb prepare dir: prot-na_10 0 katalog cp prot-na_5/* prot-na_10 cp from 5 Make rpar... close rpar prepare dir: prot-na_15 0 katalog cp prot-na_5/* prot-na_15 cp from 5 Make rpar... close rpar prepare dir: prot-na_20 0 katalog cp prot-na_5/* prot-na_20 cp from 5 Make rpar... close rpar prepare dir: prot-na_25 0 katalog cp prot-na_5/* prot-na_25 cp from 5 Make rpar... close rpar prepare dir: prot-na_30 0 katalog cp prot-na_5/* prot-na_30 cp from 5 Make rpar... close rpar gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 263 492 na-prot_1001.pdb Sterical clashes 0.534552845528 Contacts, str_name: 1 264 496 na-prot_1005.pdb Sterical clashes 0.532258064516 Contacts, str_name: 2 245 495 na-prot_1003.pdb Sterical clashes 0.494949494949 Contacts, str_name: 3 284 513 na-prot_1002.pdb Sterical clashes 0.553606237817 Contacts, str_name: 4 274 501 na-prot_1004.pdb Sterical clashes 0.546906187625 Contacts, str_name: 5 256 469 na-prot_1000.pdb Sterical clashes 0.545842217484 There are 0.53468584132 in the file prot-na_5 d_names: ['prot-na_10', 'prot-na_15', 'prot-na_20', 'prot-na_25', 'prot-na_30'] Working directory is prot-na_10 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 210 421 na-prot_1001.pdb Sterical clashes 0.498812351544 Contacts, str_name: 1 230 488 na-prot_1005.pdb Sterical clashes 0.47131147541 Contacts, str_name: 2 195 421 na-prot_1003.pdb Sterical clashes 0.463182897862 Contacts, str_name: 3 201 433 na-prot_1002.pdb Sterical clashes 0.464203233256 Contacts, str_name: 4 222 479 na-prot_1004.pdb Sterical clashes 0.463465553236 Contacts, str_name: 5 185 454 na-prot_1000.pdb Sterical clashes 0.407488986784 Working directory is prot-na_15 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 71 203 na-prot_1001.pdb Sterical clashes 0.349753694581 Contacts, str_name: 1 32 107 na-prot_1005.pdb Sterical clashes 0.299065420561 Contacts, str_name: 2 31 117 na-prot_1003.pdb Sterical clashes 0.264957264957 Contacts, str_name: 3 35 132 na-prot_1002.pdb Sterical clashes 0.265151515152 Contacts, str_name: 4 14 89 na-prot_1004.pdb Sterical clashes 0.157303370787 Contacts, str_name: 5 63 209 na-prot_1000.pdb Sterical clashes 0.301435406699 Working directory is prot-na_20 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 13 78 na-prot_1001.pdb Sterical clashes 0.166666666667 Contacts, str_name: 1 17 113 na-prot_1005.pdb Sterical clashes 0.150442477876 Contacts, str_name: 2 11 87 na-prot_1003.pdb Sterical clashes 0.126436781609 Contacts, str_name: 3 22 102 na-prot_1002.pdb Sterical clashes 0.21568627451 Contacts, str_name: 4 8 56 na-prot_1004.pdb Sterical clashes 0.142857142857 Contacts, str_name: 5 10 52 na-prot_1000.pdb Sterical clashes 0.192307692308 Working directory is prot-na_25 gramm is running, wait... ['na-prot_1001.pdb', 'na-prot_1005.pdb', 'na-prot_1003.pdb', 'na-prot_1002.pdb', 'na-prot_1004.pdb', 'na-prot_1000.pdb'] Contacts, str_name: 0 12 70 na-prot_1001.pdb Sterical clashes 0.171428571429 Contacts, str_name: 1 5 38 na-prot_1005.pdb Sterical clashes 0.131578947368 Contacts, str_name: 2 10 74 na-prot_1003.pdb Sterical clashes 0.135135135135 Contacts, str_name: 3 8 71 na-prot_1002.pdb Sterical clashes 0.112676056338 Contacts, str_name: 4 6 72 na-prot_1004.pdb Sterical clashes 0.0833333333333 Contacts, str_name: 5 11 56 na-prot_1000.pdb Sterical clashes 0.196428571429 Generating 10000 decoys first: 1 first: 1001 first: 2001 first: 3001 first: 4001 first: 5001 first: 6001 first: 7001 first: 8001 first: 9001 first: 10001 first: 11001 first: 12001 first: 13001 first: 14001 first: 15001 first: 16001 first: 17001 first: 18001 first: 19001 big_first_l, small_first_l ["ATOM 1 O5' A A 1 "] ['ATOM 1 N THR A 1 '] Sun Jul 26 18:39:39 2026 /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/prot-na_25/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/22d2d6a7-5d68-4e34-b967-3f99034261e4/prot-na_25 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt