/home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62 /home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62 /home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62 /home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62 /home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62 /home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62 n_dec 21 Thu Apr 30 01:16:04 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 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: 0 282 413 prot-na_1000.pdb Sterical clashes 0.682808716707 Contacts, str_name: 1 297 420 prot-na_1001.pdb Sterical clashes 0.707142857143 Contacts, str_name: 2 293 421 prot-na_1002.pdb Sterical clashes 0.695961995249 Contacts, str_name: 3 305 427 prot-na_1003.pdb Sterical clashes 0.714285714286 Contacts, str_name: 4 295 421 prot-na_1004.pdb Sterical clashes 0.700712589074 Contacts, str_name: 5 289 426 prot-na_1005.pdb Sterical clashes 0.678403755869 There are 0.696552604721 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 7 86 prot-na_1000.pdb Sterical clashes 0.0813953488372 Contacts, str_name: 1 9 78 prot-na_1001.pdb Sterical clashes 0.115384615385 Contacts, str_name: 2 10 66 prot-na_1002.pdb Sterical clashes 0.151515151515 Contacts, str_name: 3 9 50 prot-na_1003.pdb Sterical clashes 0.18 Contacts, str_name: 4 3 66 prot-na_1004.pdb Sterical clashes 0.0454545454545 Contacts, str_name: 5 9 55 prot-na_1005.pdb Sterical clashes 0.163636363636 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 Z 2 '] ["ATOM 1 C4' DG A 1 ", 'ATOM 227 OP2 DG B 11 '] Thu Apr 30 01:51:31 2026 /home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62/prot-na_10/*-*_*.pdb file_pdb prot-na cmd: find /home/rpdock/web/media/jobs/8402a02a-fd95-40f4-b331-d0bb29b15a62/prot-na_10 -name prot-na_*.pdb > list1.txt {'Z': []} {'A': []} run_gramm1::no filtering, list1.txt -> list.txt