Amber8 Module: ptraj ABV Successfully completed readParm. RDPARM MENU. Please enter commands. Use "?" or "help" for more info. "exit" or "quit" to leave program... RDPARM MENU: Mask [] represents 21 atoms Number: Atom Charge Mass ( Residue ) Type Tree 1: C1 -0.10100 12.0 ( 1:ABV ) ca BLA 2: C2 0.09400 12.0 ( 1:ABV ) c3 BLA 3: C3 -0.09700 12.0 ( 1:ABV ) ca BLA 4: C4 -0.09700 12.0 ( 1:ABV ) ca BLA 5: C5 -0.12500 12.0 ( 1:ABV ) ca BLA 6: C6 -0.12500 12.0 ( 1:ABV ) ca BLA 7: C7 -0.11000 12.0 ( 1:ABV ) ca BLA 8: H8 0.12500 1.0 ( 1:ABV ) ha BLA 9: H9 0.12500 1.0 ( 1:ABV ) ha BLA 10: H10 0.12800 1.0 ( 1:ABV ) ha BLA 11: H11 0.12800 1.0 ( 1:ABV ) ha BLA 12: H12 0.12700 1.0 ( 1:ABV ) ha BLA 13: O13 -0.34000 16.0 ( 1:ABV ) os BLA 14: H14 0.07900 1.0 ( 1:ABV ) h1 BLA 15: H15 0.07900 1.0 ( 1:ABV ) h1 BLA 16: C16 0.46600 12.0 ( 1:ABV ) c BLA 17: C17 -0.16600 12.0 ( 1:ABV ) c3 BLA 18: O18 -0.49300 16.0 ( 1:ABV ) o BLA 19: H19 0.09500 1.0 ( 1:ABV ) hc BLA 20: H20 0.10500 1.0 ( 1:ABV ) hc BLA 21: H21 0.10500 1.0 ( 1:ABV ) hc BLA RDPARM MENU: Mask [] represents 21 atoms Bond Kb Req atom names (numbers) 1: 335.90 1.093 :1@C2 :1@H14 (2,14) 2: 335.90 1.093 :1@C2 :1@H15 (2,15) 3: 344.30 1.087 :1@C3 :1@H8 (3,8) 4: 344.30 1.087 :1@C4 :1@H9 (4,9) 5: 344.30 1.087 :1@C5 :1@H10 (5,10) 6: 344.30 1.087 :1@C6 :1@H11 (6,11) 7: 344.30 1.087 :1@C7 :1@H12 (7,12) 8: 337.30 1.092 :1@C17 :1@H19 (17,19) 9: 337.30 1.092 :1@C17 :1@H20 (17,20) 10: 337.30 1.092 :1@C17 :1@H21 (17,21) 11: 323.50 1.513 :1@C1 :1@C2 (1,2) 12: 478.40 1.387 :1@C1 :1@C3 (1,3) 13: 478.40 1.387 :1@C1 :1@C4 (1,4) 14: 301.50 1.439 :1@C2 :1@O13 (2,13) 15: 478.40 1.387 :1@C3 :1@C5 (3,5) 16: 478.40 1.387 :1@C4 :1@C6 (4,6) 17: 478.40 1.387 :1@C5 :1@C7 (5,7) 18: 478.40 1.387 :1@C6 :1@C7 (6,7) 19: 411.30 1.343 :1@O13 :1@C16 (13,16) 20: 328.30 1.508 :1@C16 :1@C17 (16,17) 21: 648.00 1.214 :1@C16 :1@O18 (16,18) RDPARM MENU: Mask [] represents 21 atoms Angle Kthet degrees atom names (numbers) 1: 46.800 110.95 :1@C1 :1@C2 :1@H14 (1,2,14) 2: 46.800 110.95 :1@C1 :1@C2 :1@H15 (1,2,15) 3: 48.500 120.01 :1@C1 :1@C3 :1@H8 (1,3,8) 4: 48.500 120.01 :1@C1 :1@C4 :1@H9 (1,4,9) 5: 48.500 120.01 :1@C3 :1@C5 :1@H10 (3,5,10) 6: 48.500 120.01 :1@C4 :1@C6 :1@H11 (4,6,11) 7: 48.500 120.01 :1@C5 :1@C3 :1@H8 (5,3,8) 8: 48.500 120.01 :1@C5 :1@C7 :1@H12 (5,7,12) 9: 48.500 120.01 :1@C6 :1@C4 :1@H9 (6,4,9) 10: 48.500 120.01 :1@C6 :1@C7 :1@H12 (6,7,12) 11: 48.500 120.01 :1@C7 :1@C5 :1@H10 (7,5,10) 12: 48.500 120.01 :1@C7 :1@C6 :1@H11 (7,6,11) 13: 50.800 108.82 :1@O13 :1@C2 :1@H14 (13,2,14) 14: 50.800 108.82 :1@O13 :1@C2 :1@H15 (13,2,15) 15: 39.200 109.55 :1@H14 :1@C2 :1@H15 (14,2,15) 16: 47.200 109.68 :1@C16 :1@C17 :1@H19 (16,17,19) 17: 47.200 109.68 :1@C16 :1@C17 :1@H20 (16,17,20) 18: 47.200 109.68 :1@C16 :1@C17 :1@H21 (16,17,21) 19: 39.400 108.35 :1@H19 :1@C17 :1@H20 (19,17,20) 20: 39.400 108.35 :1@H19 :1@C17 :1@H21 (19,17,21) 21: 39.400 108.35 :1@H20 :1@C17 :1@H21 (20,17,21) 22: 67.700 110.51 :1@C1 :1@C2 :1@O13 (1,2,13) 23: 67.200 119.97 :1@C1 :1@C3 :1@C5 (1,3,5) 24: 67.200 119.97 :1@C1 :1@C4 :1@C6 (1,4,6) 25: 63.800 120.63 :1@C2 :1@C1 :1@C3 (2,1,3) 26: 63.800 120.63 :1@C2 :1@C1 :1@C4 (2,1,4) 27: 63.600 115.14 :1@C2 :1@O13 :1@C16 (2,13,16) 28: 67.200 119.97 :1@C3 :1@C1 :1@C4 (3,1,4) 29: 67.200 119.97 :1@C3 :1@C5 :1@C7 (3,5,7) 30: 67.200 119.97 :1@C4 :1@C6 :1@C7 (4,6,7) 31: 67.200 119.97 :1@C5 :1@C7 :1@C6 (5,7,6) 32: 69.300 111.96 :1@O13 :1@C16 :1@C17 (13,16,17) 33: 76.200 122.43 :1@O13 :1@C16 :1@O18 (13,16,18) 34: 68.000 123.11 :1@C17 :1@C16 :1@O18 (17,16,18) RDPARM MENU: Mask [] represents 21 atoms Dihedral pk phase pn atoms 1: 3.625 3.14 2.0 :1@C1 :1@C3 :1@C5 :1@H10 (1,3,5,10) 2: 3.625 3.14 2.0 :1@C1 :1@C4 :1@C6 :1@H11 (1,4,6,11) 3: 3.625 3.14 2.0 :1@C2 :1@C1 :1@C3 :1@H8 (2,1,3,8) 4: 3.625 3.14 2.0 :1@C2 :1@C1 :1@C4 :1@H9 (2,1,4,9) 5: 0.000 0.00 2.0 :1@C3 :1@C1 :1@C2 :1@H14 (3,1,2,14) 6: 0.000 0.00 2.0 :1@C3 :1@C1 :1@C2 :1@H15 (3,1,2,15) 7: 3.625 3.14 2.0 :1@C3 :1@C1 :1@C4 :1@H9 (3,1,4,9) 8: 3.625 3.14 2.0 :1@C3 :1@C5 :1@C7 :1@H12 (3,5,7,12) 9: 0.000 0.00 2.0 :1@C4 :1@C1 :1@C2 :1@H14 (4,1,2,14) 10: 0.000 0.00 2.0 :1@C4 :1@C1 :1@C2 :1@H15 (4,1,2,15) 11: 3.625 3.14 2.0 :1@C4 :1@C1 :1@C3 :1@H8 (4,1,3,8) 12: 3.625 3.14 2.0 :1@C4 :1@C6 :1@C7 :1@H12 (4,6,7,12) 13: 3.625 3.14 2.0 :1@C5 :1@C7 :1@C6 :1@H11 (5,7,6,11) 14: 3.625 3.14 2.0 :1@C6 :1@C7 :1@C5 :1@H10 (6,7,5,10) 15: 3.625 3.14 2.0 :1@C7 :1@C5 :1@C3 :1@H8 (7,5,3,8) 16: 3.625 3.14 2.0 :1@C7 :1@C6 :1@C4 :1@H9 (7,6,4,9) 17: 3.625 3.14 2.0 :1@H8 :1@C3 :1@C5 :1@H10 (8,3,5,10) 18: 3.625 3.14 2.0 :1@H9 :1@C4 :1@C6 :1@H11 (9,4,6,11) 19: 3.625 3.14 2.0 :1@H10 :1@C5 :1@C7 :1@H12 (10,5,7,12) 20: 3.625 3.14 2.0 :1@H11 :1@C6 :1@C7 :1@H12 (11,6,7,12) 21: 0.000 3.14 2.0 :1@O13 :1@C16 :1@C17 :1@H19 (13,16,17,19) 22: 0.000 3.14 2.0 :1@O13 :1@C16 :1@C17 :1@H20 (13,16,17,20) 23: 0.000 3.14 2.0 :1@O13 :1@C16 :1@C17 :1@H21 (13,16,17,21) 24: 0.383 0.00 3.0 :1@H14 :1@C2 :1@O13 :1@C16 (14,2,13,16) 25: 0.383 0.00 3.0 :1@H15 :1@C2 :1@O13 :1@C16 (15,2,13,16) 26: 0.800 0.00 1.0 :1@O18 :1@C16 :1@C17 :1@H19 (18,16,17,19) E 27: 0.080 3.14 3.0 :1@O18 :1@C16 :1@C17 :1@H19 (18,16,17,19) 28: 0.800 0.00 1.0 :1@O18 :1@C16 :1@C17 :1@H20 (18,16,17,20) E 29: 0.080 3.14 3.0 :1@O18 :1@C16 :1@C17 :1@H20 (18,16,17,20) 30: 0.800 0.00 1.0 :1@O18 :1@C16 :1@C17 :1@H21 (18,16,17,21) E 31: 0.080 3.14 3.0 :1@O18 :1@C16 :1@C17 :1@H21 (18,16,17,21) 32: 0.383 0.00 3.0 :1@C1 :1@C2 :1@O13 :1@C16 (1,2,13,16) 33: 3.625 3.14 2.0 :1@C1 :1@C3 :1@C5 :1@C7 (1,3,5,7) E 34: 3.625 3.14 2.0 :1@C1 :1@C4 :1@C6 :1@C7 (1,4,6,7) 35: 3.625 3.14 2.0 :1@C2 :1@C1 :1@C3 :1@C5 (2,1,3,5) 36: 3.625 3.14 2.0 :1@C2 :1@C1 :1@C4 :1@C6 (2,1,4,6) 37: 2.700 3.14 2.0 :1@C2 :1@O13 :1@C16 :1@C17 (2,13,16,17) 38: 1.400 3.14 1.0 :1@C2 :1@O13 :1@C16 :1@O18 (2,13,16,18) E 39: 2.700 3.14 2.0 :1@C2 :1@O13 :1@C16 :1@O18 (2,13,16,18) 40: 0.000 0.00 2.0 :1@C3 :1@C1 :1@C2 :1@O13 (3,1,2,13) 41: 3.625 3.14 2.0 :1@C3 :1@C1 :1@C4 :1@C6 (3,1,4,6) E 42: 3.625 3.14 2.0 :1@C3 :1@C5 :1@C7 :1@C6 (3,5,7,6) 43: 0.000 0.00 2.0 :1@C4 :1@C1 :1@C2 :1@O13 (4,1,2,13) 44: 3.625 3.14 2.0 :1@C4 :1@C1 :1@C3 :1@C5 (4,1,3,5) E 45: 3.625 3.14 2.0 :1@C4 :1@C6 :1@C7 :1@C5 (4,6,7,5) B 46: 1.100 3.14 2.0 :1@C2 :1@C1 :1@C4 :1@C3 (2,1,4,3) B 47: 10.500 3.14 2.0 :1@O13 :1@C17 :1@C16 :1@O18 (13,17,16,18) RDPARM MENU: No perturbed bonds RDPARM MENU: No perturbed angles RDPARM MENU: No perturbed dihedrals RDPARM MENU: The excluded atom list, NEXT is 95 C1 : C2 C3 C4 C5 C6 C7 H8 H9 H10 H11 O13 H14 H15 C16 C2 : C3 C4 C5 C6 H8 H9 O13 H14 H15 C16 C17 O18 C3 : C4 C5 C6 C7 H8 H9 H10 H12 O13 H14 H15 C4 : C5 C6 C7 H8 H9 H11 H12 O13 H14 H15 C5 : C6 C7 H8 H10 H11 H12 C6 : C7 H9 H10 H11 H12 C7 : H8 H9 H10 H11 H12 H8 : H10 H9 : H11 H10 : H12 H11 : H12 H12 : O13 : H14 H15 C16 C17 O18 H19 H20 H21 H14 : H15 C16 H15 : C16 C16 : C17 O18 H19 H20 H21 C17 : O18 H19 H20 H21 O18 : H19 H20 H21 H19 : H20 H21 H20 : H21 H21 : RDPARM MENU: Lennard-Jones Types A C c c 819971.66 531.10 c c3 924822.27 599.02 c ha 76245.15 104.66 c os 557281.14 519.16 c h1 60181.65 94.05 c o 574393.46 555.67 c hc 86154.19 112.53 c3 c3 1043080.23 675.61 c3 ha 85994.70 118.04 c3 os 628541.24 585.55 c3 h1 67877.14 106.08 c3 o 647841.73 626.72 c3 hc 97170.81 126.92 ha ha 5716.30 18.52 ha os 46871.11 97.30 ha h1 4333.25 16.31 ha o 47790.82 103.58 ha hc 6558.26 20.06 os os 361397.72 495.73 os h1 36309.72 86.62 os o 370622.49 529.25 os hc 53337.93 104.99 h1 h1 3259.70 14.31 h1 o 36947.15 92.12 h1 hc 4985.87 17.69 o o 379876.40 564.89 o hc 54426.10 111.81 hc hc 7516.08 21.73 RDPARM MENU: NOTE: if either A or C is zero (*), we cannot infer the value of r* or epsilon and assume zero... Type r* eps c 1.9080 0.0860 c3 1.9080 0.1094 ha 1.4590 0.0150 os 1.6837 0.1700 h1 1.3870 0.0157 o 1.6612 0.2100 hc 1.4870 0.0157 RDPARM MENU: The parm file was loaded originally from a file named benzylacetate.prmtop. The title is... ABV The control variables: NTOTAT is 21 (total number of atoms) NTYPES is 7 (number of atom types) NBONH is 10 (number of bonds w/ hydrogen) NBONA is 11 (number of bonds w/out hydrogen) NTHETH is 21 (number of angles w/ hydrogen) NTHETA is 13 (number of angles w/out hydrogen) NPHIH is 31 (number of dihedrals w/ hydrogen) NPHIA is 16 (number of dihedrals w/out hydrogen) NEXT is 95 (number of excluded atoms) NTOTRS is 1 (number of residues) MBONA is 11 (NBONA + number of constriant bonds) MTHETS is 13 (NTHETA + number of constraint angles) MPHIA is 16 (NPHIA + number of constraint dihedrals) MUMBND is 9 (number of unique bond types) MUMANG is 13 (number of unique angle types) MPTRA is 10 (number of unique dihedral types) NATYP is 8 (# of ``atoms'' defined in parm topo) NHB is 0 (# of type of h-bond pair interactions) IFBOX is 0 (== 1 IF periodic box info) NMXRS is 21 (number of atoms in largest residue) IFCAP is 0 (== 1 IF cap option was used in edit) IFPERT is 0 (== 1 IF perturbation info, else 0) RDPARM MENU: EXITING program...