/home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550 n_dec 21 Tue Apr 28 18:36:04 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 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 70 89 prot-na_1000.pdb Sterical clashes 0.786516853933 Contacts, str_name: 1 66 89 prot-na_1001.pdb Sterical clashes 0.741573033708 Contacts, str_name: 2 69 89 prot-na_1002.pdb Sterical clashes 0.775280898876 Contacts, str_name: 3 65 89 prot-na_1003.pdb Sterical clashes 0.730337078652 Contacts, str_name: 4 55 84 prot-na_1004.pdb Sterical clashes 0.654761904762 Contacts, str_name: 5 58 89 prot-na_1005.pdb Sterical clashes 0.651685393258 There are 0.723359193865 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 9 72 prot-na_1000.pdb Sterical clashes 0.125 Contacts, str_name: 1 4 49 prot-na_1001.pdb Sterical clashes 0.0816326530612 Contacts, str_name: 2 14 59 prot-na_1002.pdb Sterical clashes 0.237288135593 Contacts, str_name: 3 15 66 prot-na_1003.pdb Sterical clashes 0.227272727273 Contacts, str_name: 4 8 49 prot-na_1004.pdb Sterical clashes 0.163265306122 Contacts, str_name: 5 10 53 prot-na_1005.pdb Sterical clashes 0.188679245283 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 2 28 prot-na_1000.pdb Sterical clashes 0.0714285714286 Contacts, str_name: 1 1 31 prot-na_1001.pdb Sterical clashes 0.0322580645161 Contacts, str_name: 2 6 41 prot-na_1002.pdb Sterical clashes 0.146341463415 Contacts, str_name: 3 6 56 prot-na_1003.pdb Sterical clashes 0.107142857143 Contacts, str_name: 4 3 52 prot-na_1004.pdb Sterical clashes 0.0576923076923 Contacts, str_name: 5 1 34 prot-na_1005.pdb Sterical clashes 0.0294117647059 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 GLY A 1 '] ["ATOM 1 O3' A B 400 "] Tue Apr 28 19:11:23 2026 /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_15/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/629e21dd-2962-42b3-94ab-0391bc554550/prot-na_15 -name prot-na_*.pdb > list1.txt {'A': []} {'B': []} run_gramm1::no filtering, list1.txt -> list.txt