/home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67 /home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67 /home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67 /home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67 /home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67 /home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67 n_dec 21 Wed May 20 14:14:04 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 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: 0 349 726 na-prot_1001.pdb Sterical clashes 0.480716253444 Contacts, str_name: 1 382 755 na-prot_1005.pdb Sterical clashes 0.505960264901 Contacts, str_name: 2 385 756 na-prot_1003.pdb Sterical clashes 0.509259259259 Contacts, str_name: 3 378 745 na-prot_1002.pdb Sterical clashes 0.507382550336 Contacts, str_name: 4 361 733 na-prot_1004.pdb Sterical clashes 0.492496589359 Contacts, str_name: 5 434 756 na-prot_1000.pdb Sterical clashes 0.574074074074 There are 0.511648165229 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 29 137 na-prot_1001.pdb Sterical clashes 0.211678832117 Contacts, str_name: 1 50 166 na-prot_1005.pdb Sterical clashes 0.301204819277 Contacts, str_name: 2 32 142 na-prot_1003.pdb Sterical clashes 0.225352112676 Contacts, str_name: 3 24 106 na-prot_1002.pdb Sterical clashes 0.22641509434 Contacts, str_name: 4 7 100 na-prot_1004.pdb Sterical clashes 0.07 Contacts, str_name: 5 37 143 na-prot_1000.pdb Sterical clashes 0.258741258741 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 2 47 na-prot_1001.pdb Sterical clashes 0.0425531914894 Contacts, str_name: 1 3 61 na-prot_1005.pdb Sterical clashes 0.0491803278689 Contacts, str_name: 2 10 63 na-prot_1003.pdb Sterical clashes 0.15873015873 Contacts, str_name: 3 4 50 na-prot_1002.pdb Sterical clashes 0.08 Contacts, str_name: 4 7 57 na-prot_1004.pdb Sterical clashes 0.122807017544 Contacts, str_name: 5 14 101 na-prot_1000.pdb Sterical clashes 0.138613861386 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' DC A 1 "] ['ATOM 1 N SER A 69 '] Wed May 20 14:48:34 2026 /home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67/prot-na_15/*-*_*.pdb file_pdb na-prot cmd: find /home/rpdock/web/media/jobs/41381c2a-3d81-4eac-863b-b9bf50f42b67/prot-na_15 -name na-prot_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt