/home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093 n_dec 21 Mon Sep 28 06:24:02 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 Log: ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 1.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.1 step is too small for the max.(64x64x64) grid\/home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093 /home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093 /home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093 /home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093 /home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093 n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na 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... ['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: 0 355 442 prot-na_1000.pdb Sterical clashes 0.803167420814 Contacts, str_name: 1 351 442 prot-na_1001.pdb Sterical clashes 0.794117647059 Contacts, str_name: 2 335 442 prot-na_1002.pdb Sterical clashes 0.757918552036 Contacts, str_name: 3 353 442 prot-na_1003.pdb Sterical clashes 0.798642533937 Contacts, str_name: 4 319 440 prot-na_1004.pdb Sterical clashes 0.725 Contacts, str_name: 5 326 441 prot-na_1005.pdb Sterical clashes 0.739229024943 There are 0.769679196465 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: 0 279 408 prot-na_1000.pdb Sterical clashes 0.683823529412 Contacts, str_name: 1 272 418 prot-na_1001.pdb Sterical clashes 0.650717703349 Contacts, str_name: 2 299 432 prot-na_1002.pdb Sterical clashes 0.69212962963 Contacts, str_name: 3 273 436 prot-na_1003.pdb Sterical clashes 0.626146788991 Contacts, str_name: 4 268 424 prot-na_1004.pdb Sterical clashes 0.632075471698 Contacts, str_name: 5 305 441 prot-na_1005.pdb Sterical clashes 0.691609977324 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 37 229 prot-na_1000.pdb Sterical clashes 0.161572052402 Contacts, str_name: 1 19 99 prot-na_1001.pdb Sterical clashes 0.191919191919 Contacts, str_name: 2 65 178 prot-na_1002.pdb Sterical clashes 0.365168539326 Contacts, str_name: 3 23 97 prot-na_1003.pdb Sterical clashes 0.237113402062 Contacts, str_name: 4 34 189 prot-na_1004.pdb Sterical clashes 0.179894179894 Contacts, str_name: 5 47 137 prot-na_1005.pdb Sterical clashes 0.343065693431 Working directory is prot-na_20 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 26 106 prot-na_1000.pdb Sterical clashes 0.245283018868 Contacts, str_name: 1 15 95 prot-na_1001.pdb Sterical clashes 0.157894736842 Contacts, str_name: 2 9 100 prot-na_1002.pdb Sterical clashes 0.09 Contacts, str_name: 3 10 67 prot-na_1003.pdb Sterical clashes 0.149253731343 Contacts, str_name: 4 7 84 prot-na_1004.pdb Sterical clashes 0.0833333333333 Contacts, str_name: 5 15 76 prot-na_1005.pdb Sterical clashes 0.197368421053 Working directory is prot-na_25 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 15 68 prot-na_1000.pdb Sterical clashes 0.220588235294 Contacts, str_name: 1 3 52 prot-na_1001.pdb Sterical clashes 0.0576923076923 Contacts, str_name: 2 2 66 prot-na_1002.pdb Sterical clashes 0.030303030303 Contacts, str_name: 3 16 85 prot-na_1003.pdb Sterical clashes 0.188235294118 Contacts, str_name: 4 2 72 prot-na_1004.pdb Sterical clashes 0.0277777777778 Contacts, str_name: 5 5 67 prot-na_1005.pdb Sterical clashes 0.0746268656716 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 PHE A 23 '] ["ATOM 1 O5' A A 1 "] Mon Sep 28 07:00:59 2026 /home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093/prot-na_25/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/c7e459d9-fc7f-44b3-8e8b-7bcaf29aa093/prot-na_25 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt