./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.serial/dat/leap/prep to search path. > -I: Adding /usr/local/amber8.serial/dat/leap/lib to search path. > -I: Adding /usr/local/amber8.serial/dat/leap/parm to search path. > -I: Adding /usr/local/amber8.serial/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.serial/dat/leap/cmd/leaprc.gaff > ----- Source of /usr/local/amber8.serial/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /usr/local/amber8.serial/dat/leap/parm/gaff.dat ./antechamber/ash/prmtop.dif 16,20c16,20 < -3.1 1.4 1.2 1.1 1.2E+1 < -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 < 1.7 1.1E+1 -1.0E+1 8.1 -1.0E+1 --- > -2.1 1.4 1.2 1.1 6.9 > -6.7 -1.5E+1 8.2 4.1 1.9 > 6.5 -7.0 -1.4E+1 8.3 3.5 > 1.3 7.0E-1 5.0E-1 -1.8 1.9 > 1.7 6.5 -1.0E+1 8.1 -6.9 ./antechamber/ash/ash.prepin.dif 10c10 < 4 CH3 c3 M 3 2 1 1. 111. 180. -0.17 --- > 4 CH3 c3 M 3 2 1 1. 111. 180. -0.11 14,18c14,18 < 8 C c M 4 3 2 1. 158. 180. 0.66 < 9 O o E 8 4 3 1. 120. 180. -0.61 < 10 N n M 8 4 3 1. 116. 0. -0.57 < 11 H hn E 10 8 4 1. 119. 0. 0.33 < 12 CA c3 M 10 8 4 1. 121. 180. 0.05 --- > 8 C c M 4 3 2 1. 158. 180. 0.38 > 9 O o E 8 4 3 1. 120. 180. -0.36 > 10 N n M 8 4 3 1. 116. 0. -0.83 > 11 H hn E 10 8 4 1. 119. 0. 0.45 > 12 CA c3 M 10 8 4 1. 121. 180. 0.22 20,24c20,24 < 14 C2 c B 12 10 8 1. 111. -180. 0.64 < 15 O1 o E 14 12 10 1. 120. 0. -0.62 < 16 N1 n B 14 12 10 1. 116. 180. -0.55 < 17 H4 hn E 16 14 12 1. 119. 0. 0.33 < 18 C1 c3 3 16 14 12 1. 121. -180. 0.07 --- > 14 C2 c B 12 10 8 1. 111. -180. 0.36 > 15 O1 o E 14 12 10 1. 120. 0. -0.38 > 16 N1 n B 14 12 10 1. 116. 180. -0.80 > 17 H4 hn E 16 14 12 1. 119. 0. 0.45 > 18 C1 c3 3 16 14 12 1. 121. -180. 0.19 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 28,29c28,29 < 22 CB c3 M 12 10 8 1. 111. 60. -0.15 < 23 HB2 hc E 22 12 10 1. 109. -60. 0.11 --- > 22 CB c3 M 12 10 8 1. 111. 60. -0.09 > 23 HB2 hc E 22 12 10 1. 109. -60. 0.10 31,32c31,32 < 25 CG c M 22 12 10 1. 109. 179. 0.64 < 26 OD2 oh S 25 22 12 1. 117. -89. -0.60 --- > 25 CG c M 22 12 10 1. 109. 179. 0.35 > 26 OD2 oh S 25 22 12 1. 117. -89. -0.55 34c34 < 28 OD1 o M 25 22 12 1. 117. 89. -0.57 --- > 28 OD1 o M 25 22 12 1. 117. 89. -0.38 ./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.serial/dat/leap/prep to search path. > -I: Adding /usr/local/amber8.serial/dat/leap/lib to search path. > -I: Adding /usr/local/amber8.serial/dat/leap/parm to search path. > -I: Adding /usr/local/amber8.serial/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.serial/dat/leap/cmd/leaprc.gaff > ----- Source of /usr/local/amber8.serial/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /usr/local/amber8.serial/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.serial/dat/leap/prep to search path. > -I: Adding /usr/local/amber8.serial/dat/leap/lib to search path. > -I: Adding /usr/local/amber8.serial/dat/leap/parm to search path. > -I: Adding /usr/local/amber8.serial/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.serial/dat/leap/cmd/leaprc.gaff > ----- Source of /usr/local/amber8.serial/dat/leap/cmd/leaprc.gaff done 12c12 < Loading parameters: dat/leap/parm/gaff.dat --- > Loading parameters: /usr/local/amber8.serial/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 ./qmmm/standard/lysine.out.dif 71c71 < 10 -2.1110E-1 9.5830E-1 4.1484 CG 8 --- > 10 -2.1110E-1 9.5831E-1 4.1486 CG 8 83c83 < 20 -6.5331E-1 9.8858E-1 2.8940 N 1 --- > 20 -6.5331E-1 9.8861E-1 2.8942 N 1 91c91 < 20 -6.5331E-1 9.8858E-1 2.8940 N 1 --- > 20 -6.5331E-1 9.8861E-1 2.8942 N 1 ./tgtmd/change_target.ntr/tgtmd.out.dif 252c252 < 1-4 NB = 15.4663 1-4 EEL = 222.0190 VDWAALS = -2.8236 --- > 1-4 NB = 15.4663 1-4 EEL = 222.0191 VDWAALS = -2.8236 264c264 < EELEC = -238.2734 EHBOND = 0.0000 RESTRAINT = 9.4654 --- > EELEC = -238.2734 EHBOND = 0.0000 RESTRAINT = 9.4655 276c276 < EAMBER (non-restraint) = 3.5135 --- > EAMBER (non-restraint) = 3.5134 284c284 < BOND = 8.8448 ANGLE = 16.5235 DIHED = 15.2613 --- > BOND = 8.8448 ANGLE = 16.5235 DIHED = 15.2614 287c287 < EAMBER (non-restraint) = 4.6734 --- > EAMBER (non-restraint) = 4.6733 293c293 < NSTEP = 900 TIME(PS) = 1.800 TEMP(K) = 466.94 PRESS = 0.0 --- > NSTEP = 900 TIME(PS) = 1.800 TEMP(K) = 466.93 PRESS = 0.0 306c306 < BOND = 6.6787 ANGLE = 17.6617 DIHED = 14.1099 --- > BOND = 6.6787 ANGLE = 17.6618 DIHED = 14.1099 316c316 < Etot = 62.5577 EKtot = 41.5381 EPtot = 21.0196 --- > Etot = 62.5577 EKtot = 41.5381 EPtot = 21.0195 ./tgtmd/PME/tgtmd.out.dif 192c192 < Etot = -4879.0818 EKtot = 656.7986 EPtot = -5535.8804 --- > Etot = -4879.0817 EKtot = 656.7986 EPtot = -5535.8804