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@O?P Mask [:1-76@O?P] represents 150 atoms PTRAJ: donor print Atom# Residue# Name -- Atom# Residue# Name 34 2 O1P 35 2 O2P 65 3 O1P 66 3 O2P 99 4 O1P 100 4 O2P 133 5 O1P 134 5 O2P 166 6 O1P 167 6 O2P 196 7 O1P 197 7 O2P 226 8 O1P 227 8 O2P 256 9 O1P 257 9 O2P 307 10 O1P 308 10 O2P 326 11 O1P 327 11 O2P 357 12 O1P 358 12 O2P 387 13 O1P 388 13 O2P 418 14 O1P 419 14 O2P 451 15 O1P 452 15 O2P 498 16 O1P 499 16 O2P 530 17 O1P 531 17 O2P 549 18 O1P 550 18 O2P 583 19 O1P 584 19 O2P 617 20 O1P 618 20 O2P 651 21 O1P 652 21 O2P 684 22 O1P 685 22 O2P 718 23 O1P 719 23 O2P 751 24 O1P 752 24 O2P 785 25 O1P 786 25 O2P 837 26 O1P 838 26 O2P 856 27 O1P 857 27 O2P 887 28 O1P 888 28 O2P 918 29 O1P 919 29 O2P 951 30 O1P 952 30 O2P 985 31 O1P 986 31 O2P 1018 32 O1P 1019 32 O2P 1052 33 O1P 1053 33 O2P 1082 34 O1P 1083 34 O2P 1119 35 O1P 1120 35 O2P 1152 36 O1P 1153 36 O2P 1227 37 O1P 1228 37 O2P 1250 38 O1P 1251 38 O2P 1294 39 O1P 1295 39 O2P 1328 40 O1P 1329 40 O2P 1347 41 O1P 1348 41 O2P 1377 42 O1P 1378 42 O2P 1411 43 O1P 1412 43 O2P 1445 44 O1P 1446 44 O2P 1478 45 O1P 1479 45 O2P 1531 46 O1P 1532 46 O2P 1550 47 O1P 1551 47 O2P 1580 48 O1P 1581 48 O2P 1626 49 O1P 1627 49 O2P 1645 50 O1P 1646 50 O2P 1675 51 O1P 1676 51 O2P 1709 52 O1P 1710 52 O2P 1739 53 O1P 1740 53 O2P 1787 54 O1P 1788 54 O2P 1817 55 O1P 1818 55 O2P 1836 56 O1P 1837 56 O2P 1867 57 O1P 1868 57 O2P 1916 58 O1P 1917 58 O2P 1937 59 O1P 1938 59 O2P 1967 60 O1P 1968 60 O2P 1998 61 O1P 1999 61 O2P 2029 62 O1P 2030 62 O2P 2062 63 O1P 2063 63 O2P 2093 64 O1P 2094 64 O2P 2126 65 O1P 2127 65 O2P 2160 66 O1P 2161 66 O2P 2193 67 O1P 2194 67 O2P 2226 68 O1P 2227 68 O2P 2256 69 O1P 2257 69 O2P 2286 70 O1P 2287 70 O2P 2317 71 O1P 2318 71 O2P 2351 72 O1P 2352 72 O2P 2382 73 O1P 2383 73 O2P 2415 74 O1P 2416 74 O2P 2446 75 O1P 2447 75 O2P 2477 76 O1P 2478 76 O2P PTRAJ: acceptor mask :77-86@MG :77-86@MG clear PTRAJ: acceptor print PTRAJ: hbond series h1 out hbond4_.dat distance 4.0 angle -1.0 PTRAJ: radial rdf_phosphate 0.1 10.0 @MG @O?P Mask [@MG] represents 10 atoms Mask [@O?P] represents 150 atoms 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 saved to series h1, output to file hbond4_.dat, data will be sorted, intra-residue interactions will NOT be included, Distance cutoff is 4.00 angstroms, angle cutoff is -1.00 degrees Hydrogen bond information will be dumped for occupancies > 0.00 Estimated memory usage for this hbond call: 0.02 MB donors: 150 acceptors: 0 7> RADIAL DISTRIBUTION FUNCTION: Output to rdf_phosphate spacing is 0.100 maximum is 10.000 [This implies 99 bins] density is 0.033 RDF will bin all solute-mask to solvent-mask distances Solvent atom selection is :77-86 Solute atom selection is :2-76@O1P,O2P Processing AMBER trajectory file ions2test.trj.gz Set 1 .......... PTRAJ: Successfully read in 10 sets and processed 10 sets. Dumping accumulated results (if any) PTRAJ HBOND dumping summary to file hbond4_.dat PTRAJ RADIAL: dumping radial distribution functions PTRAJ: radial, density is 0.03346 density, based on volume calculation is 0.00002 Cell volume is 414364.966