/home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07 n_dec 21 Mon Feb 16 11:59:03 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\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 Log: ['\n', '*** ERROR: for prot and na molecules the 3.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 3.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for pro/home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07 /home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07 /home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07 /home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07 /home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07 t and na molecules the 3.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 3.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.1 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.2 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.2 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.3 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.3 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.4 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.4 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.5 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.5 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.6 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.6 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.7 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.7 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.8 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.8 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 4.9 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 4.9 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 5.0 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 5.0 step is too small for the max.(64x64x64) grid\n', '\n'] prot.pdb Log: ['\n', '*** ERROR: for prot and na molecules the 5.1 step is too small for the max.(64x64x64) grid\n', '\n'] ERR ['\n', '*** ERROR: for prot and na molecules the 5.1 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: 0 120 249 prot-na_1000.pdb Sterical clashes 0.481927710843 Contacts, str_name: 1 111 248 prot-na_1001.pdb Sterical clashes 0.447580645161 Contacts, str_name: 2 113 248 prot-na_1002.pdb Sterical clashes 0.45564516129 Contacts, str_name: 3 101 241 prot-na_1003.pdb Sterical clashes 0.419087136929 Contacts, str_name: 4 122 286 prot-na_1004.pdb Sterical clashes 0.426573426573 Contacts, str_name: 5 148 309 prot-na_1005.pdb Sterical clashes 0.478964401294 There are 0.451629747015 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 92 228 prot-na_1000.pdb Sterical clashes 0.40350877193 Contacts, str_name: 1 98 243 prot-na_1001.pdb Sterical clashes 0.40329218107 Contacts, str_name: 2 124 298 prot-na_1002.pdb Sterical clashes 0.41610738255 Contacts, str_name: 3 123 267 prot-na_1003.pdb Sterical clashes 0.460674157303 Contacts, str_name: 4 100 250 prot-na_1004.pdb Sterical clashes 0.4 Contacts, str_name: 5 101 211 prot-na_1005.pdb Sterical clashes 0.478672985782 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 72 192 prot-na_1000.pdb Sterical clashes 0.375 Contacts, str_name: 1 103 271 prot-na_1001.pdb Sterical clashes 0.380073800738 Contacts, str_name: 2 117 239 prot-na_1002.pdb Sterical clashes 0.489539748954 Contacts, str_name: 3 136 278 prot-na_1003.pdb Sterical clashes 0.489208633094 Contacts, str_name: 4 85 195 prot-na_1004.pdb Sterical clashes 0.435897435897 Contacts, str_name: 5 70 192 prot-na_1005.pdb Sterical clashes 0.364583333333 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 87 232 prot-na_1000.pdb Sterical clashes 0.375 Contacts, str_name: 1 112 258 prot-na_1001.pdb Sterical clashes 0.434108527132 Contacts, str_name: 2 93 212 prot-na_1002.pdb Sterical clashes 0.438679245283 Contacts, str_name: 3 111 250 prot-na_1003.pdb Sterical clashes 0.444 Contacts, str_name: 4 84 202 prot-na_1004.pdb Sterical clashes 0.415841584158 Contacts, str_name: 5 111 226 prot-na_1005.pdb Sterical clashes 0.491150442478 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: 0 106 244 prot-na_1000.pdb Sterical clashes 0.434426229508 Contacts, str_name: 1 103 237 prot-na_1001.pdb Sterical clashes 0.434599156118 Contacts, str_name: 2 69 210 prot-na_1002.pdb Sterical clashes 0.328571428571 Contacts, str_name: 3 93 212 prot-na_1003.pdb Sterical clashes 0.438679245283 Contacts, str_name: 4 104 251 prot-na_1004.pdb Sterical clashes 0.414342629482 Contacts, str_name: 5 58 155 prot-na_1005.pdb Sterical clashes 0.374193548387 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 60 174 prot-na_1000.pdb Sterical clashes 0.344827586207 Contacts, str_name: 1 89 213 prot-na_1001.pdb Sterical clashes 0.417840375587 Contacts, str_name: 2 98 254 prot-na_1002.pdb Sterical clashes 0.385826771654 Contacts, str_name: 3 95 204 prot-na_1003.pdb Sterical clashes 0.46568627451 Contacts, str_name: 4 85 198 prot-na_1004.pdb Sterical clashes 0.429292929293 Contacts, str_name: 5 61 185 prot-na_1005.pdb Sterical clashes 0.32972972973 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 4 46 prot-na_1000.pdb Sterical clashes 0.0869565217391 Contacts, str_name: 1 15 81 prot-na_1001.pdb Sterical clashes 0.185185185185 Contacts, str_name: 2 4 45 prot-na_1002.pdb Sterical clashes 0.0888888888889 Contacts, str_name: 3 8 81 prot-na_1003.pdb Sterical clashes 0.0987654320988 Contacts, str_name: 4 9 73 prot-na_1004.pdb Sterical clashes 0.123287671233 Contacts, str_name: 5 5 62 prot-na_1005.pdb Sterical clashes 0.0806451612903 Working directory is prot-na_5 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 O5' U A 1 "] Mon Feb 16 13:13:40 2026 /home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07/prot-na_5/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/c6ff895e-d08d-4e51-9c77-f5dac5fa9f07/prot-na_5 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt