/home/rpdock/web/media/jobs/a2741a2c-4dea-4d63-8106-9ddb172a0565 n_dec 21 Thu Sep 3 07:26:03 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/a2741a2c-4dea-4d63-8106-9ddb172a0565 /home/rpdock/web/media/jobs/a2741a2c-4dea-4d63-8106-9ddb172a0565 /home/rpdock/web/media/jobs/a2741a2c-4dea-4d63-8106-9ddb172a0565 /home/rpdock/web/media/jobs/a2741a2c-4dea-4d63-8106-9ddb172a0565 /home/rpdock/web/media/jobs/a2741a2c-4dea-4d63-8106-9ddb172a0565 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 Log: ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 2.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.3 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: 0 848 1271 prot-na_1000.pdb Sterical clashes 0.667191188041 Contacts, str_name: 1 851 1296 prot-na_1001.pdb Sterical clashes 0.656635802469 Contacts, str_name: 2 814 1279 prot-na_1002.pdb Sterical clashes 0.636434714621 Contacts, str_name: 3 828 1250 prot-na_1003.pdb Sterical clashes 0.6624 Contacts, str_name: 4 801 1197 prot-na_1004.pdb Sterical clashes 0.669172932331 Contacts, str_name: 5 851 1303 prot-na_1005.pdb Sterical clashes 0.653108211819 There are 0.65749047488 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: 0 780 1228 prot-na_1000.pdb Sterical clashes 0.635179153094 Contacts, str_name: 1 792 1245 prot-na_1001.pdb Sterical clashes 0.636144578313 Contacts, str_name: 2 835 1295 prot-na_1002.pdb Sterical clashes 0.644787644788 Contacts, str_name: 3 813 1311 prot-na_1003.pdb Sterical clashes 0.620137299771 Contacts, str_name: 4 890 1337 prot-na_1004.pdb Sterical clashes 0.665669409125 Contacts, str_name: 5 743 1149 prot-na_1005.pdb Sterical clashes 0.646649260226 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: 0 778 1253 prot-na_1000.pdb Sterical clashes 0.620909816441 Contacts, str_name: 1 622 1115 prot-na_1001.pdb Sterical clashes 0.557847533632 Contacts, str_name: 2 684 1184 prot-na_1002.pdb Sterical clashes 0.577702702703 Contacts, str_name: 3 732 1158 prot-na_1003.pdb Sterical clashes 0.632124352332 Contacts, str_name: 4 835 1308 prot-na_1004.pdb Sterical clashes 0.638379204893 Contacts, str_name: 5 820 1288 prot-na_1005.pdb Sterical clashes 0.636645962733 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: 0 562 971 prot-na_1000.pdb Sterical clashes 0.578784757981 Contacts, str_name: 1 716 1212 prot-na_1001.pdb Sterical clashes 0.590759075908 Contacts, str_name: 2 480 965 prot-na_1002.pdb Sterical clashes 0.497409326425 Contacts, str_name: 3 552 1000 prot-na_1003.pdb Sterical clashes 0.552 Contacts, str_name: 4 486 969 prot-na_1004.pdb Sterical clashes 0.501547987616 Contacts, str_name: 5 404 740 prot-na_1005.pdb Sterical clashes 0.545945945946 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: 0 228 580 prot-na_1000.pdb Sterical clashes 0.393103448276 Contacts, str_name: 1 311 740 prot-na_1001.pdb Sterical clashes 0.42027027027 Contacts, str_name: 2 401 771 prot-na_1002.pdb Sterical clashes 0.520103761349 Contacts, str_name: 3 228 587 prot-na_1003.pdb Sterical clashes 0.388415672913 Contacts, str_name: 4 250 512 prot-na_1004.pdb Sterical clashes 0.48828125 Contacts, str_name: 5 423 803 prot-na_1005.pdb Sterical clashes 0.526774595268 Working directory is prot-na_30 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: 0 118 311 prot-na_1000.pdb Sterical clashes 0.379421221865 Contacts, str_name: 1 130 312 prot-na_1001.pdb Sterical clashes 0.416666666667 Contacts, str_name: 2 119 312 prot-na_1002.pdb Sterical clashes 0.38141025641 Contacts, str_name: 3 76 250 prot-na_1003.pdb Sterical clashes 0.304 Contacts, str_name: 4 141 303 prot-na_1004.pdb Sterical clashes 0.465346534653 Contacts, str_name: 5 125 335 prot-na_1005.pdb Sterical clashes 0.373134328358 It is no appropriate decoys in the high resolution docking. Low resolution docking is starting! gramm scan now gramm scan now gramm scan now gramm scan now gramm scan now gramm scan now 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: 0 777 1264 prot-na_1000.pdb Sterical clashes 0.614715189873 Contacts, str_name: 1 797 1228 prot-na_1001.pdb Sterical clashes 0.649022801303 Contacts, str_name: 2 857 1313 prot-na_1002.pdb Sterical clashes 0.652703731912 Contacts, str_name: 3 764 1213 prot-na_1003.pdb Sterical clashes 0.629843363561 Contacts, str_name: 4 789 1296 prot-na_1004.pdb Sterical clashes 0.608796296296 Contacts, str_name: 5 834 1310 prot-na_1005.pdb Sterical clashes 0.636641221374 There are 0.631953767387 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 18 129 prot-na_1000.pdb Sterical clashes 0.139534883721 Contacts, str_name: 1 14 119 prot-na_1001.pdb Sterical clashes 0.117647058824 Contacts, str_name: 2 6 81 prot-na_1002.pdb Sterical clashes 0.0740740740741 Contacts, str_name: 3 4 65 prot-na_1003.pdb Sterical clashes 0.0615384615385 Contacts, str_name: 4 6 68 prot-na_1004.pdb Sterical clashes 0.0882352941176 Contacts, str_name: 5 10 96 prot-na_1005.pdb Sterical clashes 0.104166666667 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 b 3 '] ['ATOM 1 P A a 1 '] Thu Sep 3 08:36:50 2026 /home/rpdock/web/media/jobs/a2741a2c-4dea-4d63-8106-9ddb172a0565/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/a2741a2c-4dea-4d63-8106-9ddb172a0565/prot-na_10 -name prot-na_*.pdb > list1.txt {'b': []} {'a': []} run_gramm1::no filtering, list1.txt -> list.txt