/home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2 /home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2 /home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2 /home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2 /home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2 /home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2 n_dec 21 Mon Jul 6 19:32:02 2026 Checking of the smallest grid_step Log: ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 0.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 1.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.8 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 212 366 prot-na_1000.pdb Sterical clashes 0.579234972678 Contacts, str_name: 1 205 346 prot-na_1001.pdb Sterical clashes 0.592485549133 Contacts, str_name: 2 220 398 prot-na_1002.pdb Sterical clashes 0.552763819095 Contacts, str_name: 3 180 348 prot-na_1003.pdb Sterical clashes 0.51724137931 Contacts, str_name: 4 248 400 prot-na_1004.pdb Sterical clashes 0.62 Contacts, str_name: 5 216 338 prot-na_1005.pdb Sterical clashes 0.639053254438 There are 0.583463162442 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... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 10 90 prot-na_1000.pdb Sterical clashes 0.111111111111 Contacts, str_name: 1 20 136 prot-na_1001.pdb Sterical clashes 0.147058823529 Contacts, str_name: 2 31 113 prot-na_1002.pdb Sterical clashes 0.274336283186 Contacts, str_name: 3 21 108 prot-na_1003.pdb Sterical clashes 0.194444444444 Contacts, str_name: 4 21 142 prot-na_1004.pdb Sterical clashes 0.147887323944 Contacts, str_name: 5 14 95 prot-na_1005.pdb Sterical clashes 0.147368421053 Working directory is prot-na_15 gramm is running, wait... ['prot-na_1000.pdb', 'prot-na_1001.pdb', 'prot-na_1002.pdb', 'prot-na_1003.pdb', 'prot-na_1004.pdb', 'prot-na_1005.pdb'] Contacts, str_name: 0 7 61 prot-na_1000.pdb Sterical clashes 0.114754098361 Contacts, str_name: 1 5 54 prot-na_1001.pdb Sterical clashes 0.0925925925926 Contacts, str_name: 2 1 43 prot-na_1002.pdb Sterical clashes 0.0232558139535 Contacts, str_name: 3 8 87 prot-na_1003.pdb Sterical clashes 0.0919540229885 Contacts, str_name: 4 3 52 prot-na_1004.pdb Sterical clashes 0.0576923076923 Contacts, str_name: 5 8 78 prot-na_1005.pdb Sterical clashes 0.102564102564 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 N THR A 1 '] ["ATOM 1 O5' A A 1 "] Mon Jul 6 20:05:51 2026 /home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/61158ceb-9ffa-4be5-8bbc-346872939ba2/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt