Read in control variables Read in atom names... Read in charges... Read in masses... Read in IAC (atoms involved in L-J)... Read in NUMEX (index to excl atom list)... Read in NNO (index for nonbond of @type)... Read in residue labels... Read in the residue to atom pointer list... Read in bond parameters RK and REQ... Read in angle parameters TK and TEQ... Read in dihedral parameters PK, PN and PHASE... Read in SOLTY... Read in L-J parameters CN1 and CN2... Read in info for bonds w/ hydrogen... Read in info for bonds w/out hydrogen... Read in info for angles w/ hydrogen... Read in info for angles w/out hydrogen... Read in info for dihedrals w/ hydrogen... Read in info for dihedrals w/out hydrogen... Read in excluded atom list... Read in h-bond parameters: AG, BG, and HBCUT... Read in atomic symbols (types)... Read in tree information... Read in the JOIN info... Read in the IROTAT info... Read in box information... Checking coordinates: trj.5 Amber8 Module: ptraj ASP GLN ILE LEU ILE GLU ILE 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 trj.5 1 100 10 PTRAJ: donor mask :1-7@O Mask [:1-7@O] represents 7 atoms PTRAJ: acceptor WAT O H1 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 (trj.5) is an AMBER trajectory (with box info) with 100 sets (processing only 10) 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: 0.26 MB donors: 7 acceptors: 1577 Processing AMBER trajectory file trj.5 Set 1 . . . . . Set 50 . . . . . Set 100 PTRAJ: Successfully read in 100 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 | 122 :7@O | 1745 :548@H1 1744 :548@O | 30.00 2.681 ( 0.08) 22.98 ( 5.63) | 69 :4@O | 1358 :419@H1 1357 :419@O | 20.00 2.794 ( 0.08) 24.29 (12.48) | 122 :7@O | 4679 :1526@H1 4678 :1526@O | 10.00 2.831 ( 0.00) 23.68 ( 0.00) | 122 :7@O | 3482 :1127@H1 3481 :1127@O | 10.00 2.915 ( 0.00) 18.68 ( 0.00) | 122 :7@O | 3284 :1061@H1 3283 :1061@O | 10.00 2.830 ( 0.00) 11.90 ( 0.00) | 122 :7@O | 2879 :926@H1 2878 :926@O | 10.00 2.696 ( 0.00) 6.80 ( 0.00) | 122 :7@O | 2714 :871@H1 2713 :871@O | 10.00 2.770 ( 0.00) 8.79 ( 0.00) | 122 :7@O | 1385 :428@H1 1384 :428@O | 10.00 2.741 ( 0.00) 14.76 ( 0.00) | 122 :7@O | 848 :249@H1 847 :249@O | 10.00 2.631 ( 0.00) 40.39 ( 0.00) | 122 :7@O | 761 :220@H1 760 :220@O | 10.00 2.850 ( 0.00) 30.45 ( 0.00) | 122 :7@O | 368 :89@H1 367 :89@O | 10.00 2.596 ( 0.00) 21.38 ( 0.00) | 122 :7@O | 329 :76@H1 328 :76@O | 10.00 2.661 ( 0.00) 13.24 ( 0.00) | 122 :7@O | 134 :11@H1 133 :11@O | 10.00 2.915 ( 0.00) 42.17 ( 0.00) | 103 :6@O | 3689 :1196@H1 3688 :1196@O | 10.00 2.819 ( 0.00) 15.62 ( 0.00) | 103 :6@O | 3500 :1133@H1 3499 :1133@O | 10.00 2.927 ( 0.00) 25.57 ( 0.00) | 103 :6@O | 3218 :1039@H1 3217 :1039@O | 10.00 2.988 ( 0.00) 25.66 ( 0.00) | 103 :6@O | 3191 :1030@H1 3190 :1030@O | 10.00 2.965 ( 0.00) 30.13 ( 0.00) | 103 :6@O | 3011 :970@H1 3010 :970@O | 10.00 2.974 ( 0.00) 34.55 ( 0.00) | 103 :6@O | 2912 :937@H1 2911 :937@O | 10.00 2.829 ( 0.00) 4.68 ( 0.00) | 103 :6@O | 872 :257@H1 871 :257@O | 10.00 2.580 ( 0.00) 13.02 ( 0.00) | 88 :5@O | 4442 :1447@H1 4441 :1447@O | 10.00 2.733 ( 0.00) 3.99 ( 0.00) | 88 :5@O | 1097 :332@H1 1096 :332@O | 10.00 2.879 ( 0.00) 12.13 ( 0.00) | 69 :4@O | 3962 :1287@H1 3961 :1287@O | 10.00 2.866 ( 0.00) 28.55 ( 0.01) | 69 :4@O | 3002 :967@H1 3001 :967@O | 10.00 2.998 ( 0.00) 58.48 ( 0.01) | 69 :4@O | 2678 :859@H1 2677 :859@O | 10.00 2.832 ( 0.00) 30.37 ( 0.00) | 69 :4@O | 2651 :850@H1 2650 :850@O | 10.00 2.780 ( 0.00) 25.89 ( 0.00) | 50 :3@O | 4724 :1541@H1 4723 :1541@O | 10.00 2.728 ( 0.00) 7.49 ( 0.00) | 50 :3@O | 869 :256@H1 868 :256@O | 10.00 2.782 ( 0.00) 43.80 ( 0.00) | 50 :3@O | 281 :60@H1 280 :60@O | 10.00 2.997 ( 0.00) 23.14 ( 0.00) | 31 :2@O | 4430 :1443@H1 4429 :1443@O | 10.00 2.831 ( 0.00) 26.73 ( 0.00) | 31 :2@O | 3989 :1296@H1 3988 :1296@O | 10.00 2.843 ( 0.00) 29.55 ( 0.00) | 31 :2@O | 3725 :1208@H1 3724 :1208@O | 10.00 2.524 ( 0.00) 22.80 ( 0.01) | 31 :2@O | 3056 :985@H1 3055 :985@O | 10.00 2.976 ( 0.00) 24.72 ( 0.00) | 31 :2@O | 2363 :754@H1 2362 :754@O | 10.00 2.660 ( 0.00) 12.65 ( 0.00) | 31 :2@O | 2318 :739@H1 2317 :739@O | 10.00 2.581 ( 0.00) 11.79 ( 0.00) | 31 :2@O | 1445 :448@H1 1444 :448@O | 10.00 2.855 ( 0.00) 42.22 ( 0.01) | 31 :2@O | 1391 :430@H1 1390 :430@O | 10.00 2.560 ( 0.00) 21.82 ( 0.00) | 14 :1@O | 3779 :1226@H1 3778 :1226@O | 10.00 2.876 ( 0.00) 15.90 ( 0.00) | 14 :1@O | 3725 :1208@H1 3724 :1208@O | 10.00 2.729 ( 0.00) 19.22 ( 0.00) | 14 :1@O | 1529 :476@H1 1528 :476@O | 10.00 2.965 ( 0.00) 7.70 ( 0.00) | 14 :1@O | 1172 :357@H1 1171 :357@O | 10.00 2.912 ( 0.00) 26.75 ( 0.00) ---------------- --------------------------------- -------------------------------------