log started: Thu Nov 18 09:47:42 2010 Log file: ./solvents.log > # > # load water models > # > > addAtomTypes { > { "HW" "H" "sp3" } > { "OW" "O" "sp3" } > { "EP" "Lp" "sp3" } > } > > # > # TIP3 water > # > > h1 = createAtom H1 HW 0.417 > h2 = createAtom H2 HW 0.417 > o = createAtom O OW -0.834 > > set h1 element H > set h2 element H > set o element O > > r = createResidue WAT > add r o > add r h1 > add r h2 > > bond h1 o > bond h2 o > bond h1 h2 > > TP3 = createUnit TP3 > > add TP3 r > set TP3.1 restype solvent > set TP3.1 imagingAtom TP3.1.O > > zMatrix TP3 { > { H1 O 0.9572 } > { H2 O H1 0.9572 104.52 } > } > > # > # TIP3(F) water > # > > h1 = createAtom H1 HW 0.415 > h2 = createAtom H2 HW 0.415 > o = createAtom O OW -0.830 > > set h1 element H > set h2 element H > set o element O > > r = createResidue WAT > add r o > add r h1 > add r h2 > > bond h1 o > bond h2 o > bond h1 h2 > > TPF = createUnit TPF > > add TPF r > set TPF.1 restype solvent > set TPF.1 imagingAtom TPF.1.O > > zMatrix TPF { > { H1 O 0.9572 } > { H2 O H1 0.9572 104.52 } > } > > # > # SPC/E water > # > > h1 = createAtom H1 HW 0.4238 > h2 = createAtom H2 HW 0.4238 > o = createAtom O OW -0.8476 > > set h1 element H > set h2 element H > set o element O > > r = createResidue WAT > add r o > add r h1 > add r h2 > > bond h1 o > bond h2 o > bond h1 h2 > > SPC = createUnit SPC > > add SPC r > set SPC.1 restype solvent > set SPC.1 imagingAtom SPC.1.O > > zMatrix SPC { > { H1 O 1.0000 } > { H2 O H1 1.0000 109.47 } > } > > > # > # SPC/Fw water, JCP 124:024503 (2006) > # > > h1 = createAtom H1 HW 0.41 > h2 = createAtom H2 HW 0.41 > o = createAtom O OW -0.82 > > set h1 element H > set h2 element H > set o element O > > r = createResidue WAT > add r o > add r h1 > add r h2 > > bond h1 o > bond h2 o > bond h1 h2 > > SPF = createUnit SPF > > add SPF r > set SPF.1 restype solvent > set SPF.1 imagingAtom SPF.1.O > > zMatrix SPF { > { H1 O 1.0120 } > { H2 O H1 1.0120 113.24 } > } > > > # > # qSPC/Fw water, JCP 125:184057 (2006) > # > > h1 = createAtom H1 HW 0.42 > h2 = createAtom H2 HW 0.42 > o = createAtom O OW -0.84 > > set h1 element H > set h2 element H > set o element O > > r = createResidue WAT > add r o > add r h1 > add r h2 > > bond h1 o > bond h2 o > bond h1 h2 > > SPG = createUnit SPG > > add SPG r > set SPG.1 restype solvent > set SPG.1 imagingAtom SPG.1.O > > zMatrix SPG { > { H1 O 1.0000 } > { H2 O H1 1.0000 112.00 } > } > > > # > # POL3 water > # > > h1 = createAtom H1 HW 0.3650 > h2 = createAtom H2 HW 0.3650 > o = createAtom O OW -0.7300 > > set h1 element H > set h2 element H > set o element O > > r = createResidue WAT > add r o > add r h1 > add r h2 > > bond h1 o > bond h2 o > bond h1 h2 > > PL3 = createUnit PL3 > > add PL3 r > set PL3.1 restype solvent > set PL3.1 imagingAtom PL3.1.O > > zMatrix PL3 { > { H1 O 1.0000 } > { H2 O H1 1.0000 109.47 } > } > > # > # TIP4P water > # > > h1 = createAtom H1 HW 0.52 > h2 = createAtom H2 HW 0.52 > o = createAtom O OW 0.0 > ep = createAtom EPW EP -1.04 > > set h1 element H > set h2 element H > set o element O > set ep element Lp > > r = createResidue WAT > add r o > add r h1 > add r h2 > add r ep > > bond h1 o > bond h2 o > bond h1 h2 > bond ep o > > TP4 = createUnit TP4 > > add TP4 r > set TP4.1 restype solvent > set TP4.1 imagingAtom TP4.1.O > > zMatrix TP4 { > { H1 O 0.9572 } > { H2 O H1 0.9572 104.52 } > { EPW O H1 H2 0.15 52.26 0.0 } > } > > # > # TIP4P-Ew water (Ewald modified TIP4P) > # > > h1 = createAtom H1 HW 0.52422 > h2 = createAtom H2 HW 0.52422 > o = createAtom O OW 0.0 > ep = createAtom EPW EP -1.04844 > > set h1 element H > set h2 element H > set o element O > set ep element Lp > > r = createResidue WAT > add r o > add r h1 > add r h2 > add r ep > > bond h1 o > bond h2 o > bond h1 h2 > bond ep o > > T4E = createUnit T4E > > add T4E r > set T4E.1 restype solvent > set T4E.1 imagingAtom T4E.1.O > > zMatrix T4E { > { H1 O 0.9572 } > { H2 O H1 0.9572 104.52 } > { EPW O H1 H2 0.125 52.26 0.0 } > } > > # > # Dang-Chang (JCP 106:8149, 1997) water (DC4) > # > > h1 = createAtom H1 HW 0.519 > h2 = createAtom H2 HW 0.519 > o = createAtom O OW 0.0 > ep = createAtom EPW EP -1.038 > > set h1 element H > set h2 element H > set o element O > set ep element Lp > > r = createResidue WAT > add r o > add r h1 > add r h2 > add r ep > > bond h1 o > bond h2 o > bond h1 h2 > bond ep o > > DC4 = createUnit DC4 > > add DC4 r > set DC4.1 restype solvent > set DC4.1 imagingAtom DC4.1.O > > zMatrix DC4 { > { H1 O 0.9572 } > { H2 O H1 0.9572 104.52 } > { EPW O H1 H2 0.215 52.26 0.0 } > } > > # > # TIP5P water > # > > h1 = createAtom H1 HW 0.2410 > h2 = createAtom H2 HW 0.2410 > o = createAtom O OW 0.0 > ep1 = createAtom EP1 EP -0.241 > ep2 = createAtom EP2 EP -0.241 > > set h1 element H > set h2 element H > set o element O > set ep1 element Lp > set ep2 element Lp > > r = createResidue WAT > add r o > add r h1 > add r h2 > add r ep1 > add r ep2 > > bond h1 o > bond h2 o > bond h1 h2 > bond ep1 o > bond ep2 o > > TP5 = createUnit TP5 > > add TP5 r > set TP5.1 restype solvent > set TP5.1 imagingAtom TP5.1.O > > zMatrix TP5 { > { H1 O 0.9572 } > { H2 O H1 0.9572 104.52 } > { EP1 O H1 H2 0.70 109.47 -90. } > { EP2 O H1 H2 0.70 109.47 90. } > } > > > loadOff ./tip3pbox.off Loading library: ./tip3pbox.off Loading: TIP3PBOX > loadOff ./tip3pfbox.off Loading library: ./tip3pfbox.off Loading: TIP3PFBOX > loadOff ./tip4pbox.off Loading library: ./tip4pbox.off Loading: TIP4PBOX > loadOff ./tip4pewbox.off Loading library: ./tip4pewbox.off Loading: TIP4PEWBOX > loadOff ./pol3box.off Loading library: ./pol3box.off Loading: POL3BOX > loadOff ./spcebox.off Loading library: ./spcebox.off Loading: SPCBOX > loadOff ./spcfwbox.off Loading library: ./spcfwbox.off Loading: SPCFWBOX > loadOff ./qspcfwbox.off Loading library: ./qspcfwbox.off Loading: QSPCFWBOX > loadOff ./chcl3box.off Loading library: ./chcl3box.off Loading: CHCL3BOX > loadOff ./meohbox.off Loading library: ./meohbox.off Loading: MEOHBOX > loadOff ./nmabox.off Loading library: ./nmabox.off Loading: NMABOX > > a = { TP3 TPF SPC TP4 T4E DC4 TP5 PL3 SPF SPG TIP3PBOX TIP3PFBOX TIP4PBOX TIP4PEWBOX SPCBOX QSPCFWBOX SPCFWBOX POL3BOX CHCL3BOX MEOHBOX NMABOX } > saveOff a ./solvents.lib Saving TP3. Building topology. Building atom parameters. Saving TPF. Building topology. Building atom parameters. Saving SPC. Building topology. Building atom parameters. Saving TP4. Building topology. Building atom parameters. Saving T4E. Building topology. Building atom parameters. Saving DC4. Building topology. Building atom parameters. Saving TP5. Building topology. Building atom parameters. Saving PL3. Building topology. Building atom parameters. Saving SPF. Building topology. Building atom parameters. Saving SPG. Building topology. Building atom parameters. Saving TIP3PBOX. Building topology. Building atom parameters. Saving TIP3PFBOX. Building topology. Building atom parameters. Saving TIP4PBOX. Building topology. Building atom parameters. Saving TIP4PEWBOX. Building topology. Building atom parameters. Saving SPCBOX. Building topology. Building atom parameters. Saving QSPCFWBOX. Building topology. Building atom parameters. Saving SPCFWBOX. Building topology. Building atom parameters. Saving POL3BOX. Building topology. Building atom parameters. Saving CHCL3BOX. Building topology. Building atom parameters. Saving MEOHBOX. Building topology. Building atom parameters. Saving NMABOX. Building topology. Building atom parameters. > > quit Quit