/home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11 n_dec 21 Mon Sep 28 09:38:01 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/f7013d68-6b34-49b0-8df9-a432b0fb0c11 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11 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: 0 334 441 prot-na_1000.pdb Sterical clashes 0.757369614512 Contacts, str_name: 1 347 442 prot-na_1001.pdb Sterical clashes 0.785067873303 Contacts, str_name: 2 329 442 prot-na_1002.pdb Sterical clashes 0.744343891403 Contacts, str_name: 3 327 441 prot-na_1003.pdb Sterical clashes 0.741496598639 Contacts, str_name: 4 344 442 prot-na_1004.pdb Sterical clashes 0.778280542986 Contacts, str_name: 5 345 438 prot-na_1005.pdb Sterical clashes 0.787671232877 There are 0.765704958953 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: 0 296 429 prot-na_1000.pdb Sterical clashes 0.689976689977 Contacts, str_name: 1 283 426 prot-na_1001.pdb Sterical clashes 0.664319248826 Contacts, str_name: 2 228 409 prot-na_1002.pdb Sterical clashes 0.557457212714 Contacts, str_name: 3 269 421 prot-na_1003.pdb Sterical clashes 0.638954869359 Contacts, str_name: 4 330 442 prot-na_1004.pdb Sterical clashes 0.746606334842 Contacts, str_name: 5 277 432 prot-na_1005.pdb Sterical clashes 0.641203703704 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 28 176 prot-na_1000.pdb Sterical clashes 0.159090909091 Contacts, str_name: 1 31 138 prot-na_1001.pdb Sterical clashes 0.224637681159 Contacts, str_name: 2 20 166 prot-na_1002.pdb Sterical clashes 0.120481927711 Contacts, str_name: 3 61 147 prot-na_1003.pdb Sterical clashes 0.414965986395 Contacts, str_name: 4 21 146 prot-na_1004.pdb Sterical clashes 0.143835616438 Contacts, str_name: 5 54 146 prot-na_1005.pdb Sterical clashes 0.369863013699 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 8 70 prot-na_1000.pdb Sterical clashes 0.114285714286 Contacts, str_name: 1 21 77 prot-na_1001.pdb Sterical clashes 0.272727272727 Contacts, str_name: 2 11 79 prot-na_1002.pdb Sterical clashes 0.139240506329 Contacts, str_name: 3 9 64 prot-na_1003.pdb Sterical clashes 0.140625 Contacts, str_name: 4 13 83 prot-na_1004.pdb Sterical clashes 0.156626506024 Contacts, str_name: 5 6 55 prot-na_1005.pdb Sterical clashes 0.109090909091 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 11 84 prot-na_1000.pdb Sterical clashes 0.130952380952 Contacts, str_name: 1 8 79 prot-na_1001.pdb Sterical clashes 0.101265822785 Contacts, str_name: 2 11 90 prot-na_1002.pdb Sterical clashes 0.122222222222 Contacts, str_name: 3 7 74 prot-na_1003.pdb Sterical clashes 0.0945945945946 Contacts, str_name: 4 8 70 prot-na_1004.pdb Sterical clashes 0.114285714286 Contacts, str_name: 5 4 74 prot-na_1005.pdb Sterical clashes 0.0540540540541 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 10:14:57 2026 /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_25/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/f7013d68-6b34-49b0-8df9-a432b0fb0c11/prot-na_25 -name prot-na_*.pdb > list1.txt {'A': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt