Amber8 Module: ptraj RG5 RC RG RG RA RU RU RU RA 2MG RC RU RC RA RG H2U H2U RG RG RG RA RG RA RG RC M2G RC RC RA RG RA OMC RU OMG RA RA YG RA PSU 5MC RU RG RG RA RG 7MG RU RC 5MC RU RG RU RG 5MU PSU RC RG 1MA RU RC RC RA RC RA RG RA RA RU RU RC RG RC RA RC RC RA3 MG MG MG MG MG MG MG MG MG MG SPM Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ ... Na+ WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT ... WAT Scanning Box Successfully completed readParm. PTRAJ: Processing input file... Input is from standard input PTRAJ: trajin ions2test.trj.gz PTRAJ: donor mask :1-76@O1P Mask [:1-76@O1P] represents 75 atoms PTRAJ: donor print Atom# Residue# Name -- Atom# Residue# Name 34 2 O1P 65 3 O1P 99 4 O1P 133 5 O1P 166 6 O1P 196 7 O1P 226 8 O1P 256 9 O1P 307 10 O1P 326 11 O1P 357 12 O1P 387 13 O1P 418 14 O1P 451 15 O1P 498 16 O1P 530 17 O1P 549 18 O1P 583 19 O1P 617 20 O1P 651 21 O1P 684 22 O1P 718 23 O1P 751 24 O1P 785 25 O1P 837 26 O1P 856 27 O1P 887 28 O1P 918 29 O1P 951 30 O1P 985 31 O1P 1018 32 O1P 1052 33 O1P 1082 34 O1P 1119 35 O1P 1152 36 O1P 1227 37 O1P 1250 38 O1P 1294 39 O1P 1328 40 O1P 1347 41 O1P 1377 42 O1P 1411 43 O1P 1445 44 O1P 1478 45 O1P 1531 46 O1P 1550 47 O1P 1580 48 O1P 1626 49 O1P 1645 50 O1P 1675 51 O1P 1709 52 O1P 1739 53 O1P 1787 54 O1P 1817 55 O1P 1836 56 O1P 1867 57 O1P 1916 58 O1P 1937 59 O1P 1967 60 O1P 1998 61 O1P 2029 62 O1P 2062 63 O1P 2093 64 O1P 2126 65 O1P 2160 66 O1P 2193 67 O1P 2226 68 O1P 2256 69 O1P 2286 70 O1P 2317 71 O1P 2351 72 O1P 2382 73 O1P 2415 74 O1P 2446 75 O1P 2477 76 O1P PTRAJ: acceptor MG MG MG PTRAJ: acceptor print Atom# Residue# Name -- Atom# Residue# Name 2510 77 MG -- 2510 77 MG 2511 78 MG -- 2511 78 MG 2512 79 MG -- 2512 79 MG 2513 80 MG -- 2513 80 MG 2514 81 MG -- 2514 81 MG 2515 82 MG -- 2515 82 MG 2516 83 MG -- 2516 83 MG 2517 84 MG -- 2517 84 MG 2518 85 MG -- 2518 85 MG 2519 86 MG -- 2519 86 MG PTRAJ: hbond FYI: No output trajectory specified (trajout), none will be saved. PTRAJ: Successfully read the input file. Coordinate processing will occur on 10 frames. Summary of I/O and actions follows: INPUT COORDINATE FILES File (ions2test.trj.gz) is an AMBER trajectory (with box info) with 10 sets OUTPUT COORDINATE FILE NULL entry ACTIONS 1> HBOND data will be sorted, intra-residue interactions will NOT be included, Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees Hydrogen bond information will be dumped for occupancies > 0.00 Estimated memory usage for this hbond call: 0.02 MB donors: 75 acceptors: 10 Processing AMBER trajectory file ions2test.trj.gz Set 1 .......... PTRAJ: Successfully read in 10 sets and processed 10 sets. Dumping accumulated results (if any) HBOND SUMMARY: data was sorted, intra-residue interactions are NOT included, Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees Hydrogen bond information dumped for occupancies > 0.00 DONOR ACCEPTORH ACCEPTOR atom# :res@atom atom# :res@atom atom# :res@atom %occupied distance angle ---------------- --------------------------------- -------------------------------------