./antechamber/ash/leap.out.dif 1,4c1,4 < -I: Adding dat/leap/prep to search path. < -I: Adding dat/leap/lib to search path. < -I: Adding dat/leap/parm to search path. < -I: Adding dat/leap/cmd to search path. --- > -I: Adding /usr/local/amber8.lammpi/dat/leap/prep to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/lib to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/parm to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/cmd to search path. 9,10c9,10 < ----- Source: dat/leap/cmd/leaprc.gaff < ----- Source of dat/leap/cmd/leaprc.gaff done --- > ----- Source: /usr/local/amber8.lammpi/dat/leap/cmd/leaprc.gaff > ----- Source of /usr/local/amber8.lammpi/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /usr/local/amber8.lammpi/dat/leap/parm/gaff.dat ./antechamber/ash/prmtop.dif 17,19c17,19 < -1.1E+1 -1.0E+1 6.1 9.4E-1 1.8 < 1.1E+1 -1.1E+1 -1.0E+1 6.1 1.4 < 1.3 7.4E-1 4.9E-1 -2.8 2.0 --- > -1.1E+1 -1.0E+1 6.1 9.2E-1 1.9 > 1.1E+1 -1.1E+1 -1.0E+1 6.1 1.3 > 1.3 7.0E-1 5.0E-1 -2.8 1.9 ./antechamber/ash/ash.prepin.dif 15c15 < 9 O o E 8 4 3 1. 120. 180. -0.61 --- > 9 O o E 8 4 3 1. 120. 180. -0.60 20c20 < 14 C2 c B 12 10 8 1. 111. -180. 0.64 --- > 14 C2 c B 12 10 8 1. 111. -180. 0.63 26c26 < 20 H2 h1 E 18 16 14 1. 109. 120. 0.04 --- > 20 H2 h1 E 18 16 14 1. 109. 120. 0.03 29c29 < 23 HB2 hc E 22 12 10 1. 109. -60. 0.11 --- > 23 HB2 hc E 22 12 10 1. 109. -60. 0.10 ./antechamber/sustiva/leap.out.dif 1,4c1,4 < -I: Adding dat/leap/prep to search path. < -I: Adding dat/leap/lib to search path. < -I: Adding dat/leap/parm to search path. < -I: Adding dat/leap/cmd to search path. --- > -I: Adding /usr/local/amber8.lammpi/dat/leap/prep to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/lib to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/parm to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/cmd to search path. 9,10c9,10 < ----- Source: dat/leap/cmd/leaprc.gaff < ----- Source of dat/leap/cmd/leaprc.gaff done --- > ----- Source: /usr/local/amber8.lammpi/dat/leap/cmd/leaprc.gaff > ----- Source of /usr/local/amber8.lammpi/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /usr/local/amber8.lammpi/dat/leap/parm/gaff.dat ./antechamber/sustiva/sustiva.prepin.dif 29c29 < 23 F3 f E 20 19 18 1.3 111.5 -58.5 -0.214 --- > 23 F3 f E 20 19 18 1.3 111.5 -58.5 -0.215 ./antechamber/sustiva/prmtop.dif 16c16 < -3.24 -9.05E-1 3.08 -3.48E-1 -1.36 --- > -3.25 -9.02E-1 3.08 -3.49E-1 -1.36 21c21 < 1.46 1.50 -2.04 1.44 1.47 --- > 1.46 1.51 -2.05 1.44 1.47 ./antechamber/tp/prmtop.mol2.dif 15,16c15,16 < -2.15 -2.07 3.00E-1 -2.49 -2.64 < -2.04 2.35 -4.64 3.48 2.45 --- > -2.15 -2.07 2.98E-1 -2.49 -2.64 > -2.04 2.35 -4.63 3.48 2.45 ./antechamber/tp/prmtop.dif 15c15 < -2.15 2.61 -2.07 2.45 -2.49 --- > -2.15 2.60 -2.07 2.45 -2.49 17c17 < 3.00E-1 -4.64 3.48 --- > 2.98E-1 -4.63 3.48 ./antechamber/guanine_amber/DGN.prepin.dif 12c12 < 6 C5' CT M 4 3 2 1.4 35.6 -117.6 0.115 --- > 6 C5' CT M 4 3 2 1.4 35.6 -117.6 0.114 36c36 < 30 C2 CA M 28 26 25 1.3 125.2 -0.1 0.678 --- > 30 C2 CA M 28 26 25 1.3 125.2 -0.1 0.677 40c40 < 34 N3 NC M 30 28 26 1.3 123.3 0.0 -0.674 --- > 34 N3 NC M 30 28 26 1.3 123.3 0.0 -0.673 ./antechamber/guanine/leap.out.dif 1,4c1,4 < -I: Adding dat/leap/prep to search path. < -I: Adding dat/leap/lib to search path. < -I: Adding dat/leap/parm to search path. < -I: Adding dat/leap/cmd to search path. --- > -I: Adding /usr/local/amber8.lammpi/dat/leap/prep to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/lib to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/parm to search path. > -I: Adding /usr/local/amber8.lammpi/dat/leap/cmd to search path. 9,10c9,10 < ----- Source: dat/leap/cmd/leaprc.gaff < ----- Source of dat/leap/cmd/leaprc.gaff done --- > ----- Source: /usr/local/amber8.lammpi/dat/leap/cmd/leaprc.gaff > ----- Source of /usr/local/amber8.lammpi/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /usr/local/amber8.lammpi/dat/leap/parm/gaff.dat ./antechamber/fluorescein/fluorescein.prepin.dif 39,40c39,40 < 33 C23 ca M 31 29 27 1.3 119.4 -0.0 -0.118 < 34 H33 ha E 33 31 29 1.0 121.3 -179.9 0.155 --- > 33 C23 ca M 31 29 27 1.3 119.4 -0.0 -0.117 > 34 H33 ha E 33 31 29 1.0 121.3 -179.9 0.156 ./antechamber/fluorescein/prmtop.dif 7c7 < 180 1 28 41 59 13 22 7 7 0 --- > 180 1 28 41 59 13 22 8 7 0 81c81 < 2.8 1.0E+1 --- > 2.8 1.0E+1 1.1 85c85 < 2.0 2.0 --- > 2.0 2.0 2.0 89c89 < 3.1 3.1 --- > 3.1 3.1 3.1 198c198 < 93 99 -96 -102 7 --- > 93 99 -96 -102 8 ./pheTI/out.p1.dif 190c190 < Ewald error estimate: 0.5094E-16 --- > Ewald error estimate: 0.0000 ./tgtmd/PME/tgtmd.out.dif 192c192 < Etot = -4879.0818 EKtot = 656.7986 EPtot = -5535.8804 --- > Etot = -4879.0817 EKtot = 656.7986 EPtot = -5535.8804 ./trx/mdout.trx.cpln.dif 113c113 < EELEC = -55078.4222 EHBOND = 0.0000 RESTRAINT = 0.0000 --- > EELEC = -55078.4221 EHBOND = 0.0000 RESTRAINT = 0.0000