log started: Thu Nov 18 09:41:17 2010 Log file: ./ions94.log > # > # Monovalent, monoatomic ions using '94 atom types. > # The Li+..Cs+ series uses types derived from the > # work of Aqvist (see force field documentation). > # IB (ion+water) is a hack for vacuum modeling. > # > > i = createAtom Li+ Li 1.0 > set i element Li > set i position { 0 0 0 } > r = createResidue Li+ > add r i > Li+ = createUnit Li+ > add Li+ r > saveOff Li+ ./ions94.lib Creating ./ions94.lib Saving Li+. Building topology. Building atom parameters. > > i = createAtom Na+ IP 1.0 > set i element Na > set i position { 0 0 0 } > r = createResidue CIO > add r i > CIO = createUnit CIO > add CIO r > saveOff CIO ./ions94.lib Saving CIO. Building topology. Building atom parameters. > > i = createAtom Na+ IP 1.0 > set i element Na > set i position { 0 0 0 } > r = createResidue Na+ > add r i > Na+ = createUnit Na+ > add Na+ r > saveOff Na+ ./ions94.lib Saving Na+. Building topology. Building atom parameters. > > i = createAtom K+ K 1.0 > set i element K > set i position { 0 0 0 } > r = createResidue K+ > add r i > K+ = createUnit K+ > add K+ r > saveOff K+ ./ions94.lib Saving K+. Building topology. Building atom parameters. > > i = createAtom Rb+ Rb 1.0 > set i element Rb > set i position { 0 0 0 } > r = createResidue Rb+ > add r i > Rb+ = createUnit Rb+ > add Rb+ r > saveOff Rb+ ./ions94.lib Saving Rb+. Building topology. Building atom parameters. > > i = createAtom Cs+ Cs 1.0 > set i element Cs > set i position { 0 0 0 } > r = createResidue Cs+ > add r i > Cs+ = createUnit Cs+ > add Cs+ r > saveOff Cs+ ./ions94.lib Saving Cs+. Building topology. Building atom parameters. > > i = createAtom Cl- IM -1.0 > set i element Cl > set i position { 0 0 0 } > r = createResidue Cl- > add r i > Cl- = createUnit Cl- > add Cl- r > saveOff Cl- ./ions94.lib Saving Cl-. Building topology. Building atom parameters. > > i = createAtom MG MG 2.0 > set i element Mg > set i position { 0 0 0 } > r = createResidue MG2 > add r i > MG2 = createUnit MG2 > add MG2 r > saveOff MG2 ./ions94.lib Saving MG2. Building topology. Building atom parameters. > > i = createAtom IB IB 1.0 > set i element Cs > set i position { 0 0 0 } > r = createResidue IB > add r i > IB = createUnit IB > add IB r > saveOff IB ./ions94.lib Saving IB. Building topology. Building atom parameters. > quit Quit log started: Thu Nov 18 09:41:17 2010 Log file: ./ions94.log > # > # Monovalent, monoatomic ions using '94 atom types. > # The Li+..Cs+ series uses types derived from the > # work of Aqvist (see force field documentation). > # IB (ion+water) is a hack for vacuum modeling. > # > > i = createAtom Li+ Li 1.0 > set i element Li > set i position { 0 0 0 } > r = createResidue Li+ > add r i > Li+ = createUnit Li+ > add Li+ r > saveOff Li+ ./ions94.lib Saving Li+. Building topology. Building atom parameters. > > i = createAtom Na+ IP 1.0 > set i element Na > set i position { 0 0 0 } > r = createResidue CIO > add r i > CIO = createUnit CIO > add CIO r > saveOff CIO ./ions94.lib Saving CIO. Building topology. Building atom parameters. > > i = createAtom Na+ IP 1.0 > set i element Na > set i position { 0 0 0 } > r = createResidue Na+ > add r i > Na+ = createUnit Na+ > add Na+ r > saveOff Na+ ./ions94.lib Saving Na+. Building topology. Building atom parameters. > > i = createAtom K+ K 1.0 > set i element K > set i position { 0 0 0 } > r = createResidue K+ > add r i > K+ = createUnit K+ > add K+ r > saveOff K+ ./ions94.lib Saving K+. Building topology. Building atom parameters. > > i = createAtom Rb+ Rb 1.0 > set i element Rb > set i position { 0 0 0 } > r = createResidue Rb+ > add r i > Rb+ = createUnit Rb+ > add Rb+ r > saveOff Rb+ ./ions94.lib Saving Rb+. Building topology. Building atom parameters. > > i = createAtom Cs+ Cs 1.0 > set i element Cs > set i position { 0 0 0 } > r = createResidue Cs+ > add r i > Cs+ = createUnit Cs+ > add Cs+ r > saveOff Cs+ ./ions94.lib Saving Cs+. Building topology. Building atom parameters. > > i = createAtom Cl- IM -1.0 > set i element Cl > set i position { 0 0 0 } > r = createResidue Cl- > add r i > Cl- = createUnit Cl- > add Cl- r > saveOff Cl- ./ions94.lib Saving Cl-. Building topology. Building atom parameters. > > i = createAtom MG MG 2.0 > set i element Mg > set i position { 0 0 0 } > r = createResidue MG2 > add r i > MG2 = createUnit MG2 > add MG2 r > saveOff MG2 ./ions94.lib Saving MG2. Building topology. Building atom parameters. > > i = createAtom IB IB 1.0 > set i element Cs > set i position { 0 0 0 } > r = createResidue IB > add r i > IB = createUnit IB > add IB r > saveOff IB ./ions94.lib Saving IB. Building topology. Building atom parameters. > quit Quit log started: Thu Nov 18 09:47:42 2010 Log file: ./ions94.log > # > # Monovalent, monoatomic ions using '94 atom types. > # The Li+..Cs+ series uses types derived from the > # work of Aqvist (see force field documentation). > # IB (ion+water) is a hack for vacuum modeling. > # > > i = createAtom Li+ Li 1.0 > set i element Li > set i position { 0 0 0 } > r = createResidue Li+ > add r i > Li+ = createUnit Li+ > add Li+ r > saveOff Li+ ./ions94.lib Saving Li+. Building topology. Building atom parameters. > > i = createAtom Na+ IP 1.0 > set i element Na > set i position { 0 0 0 } > r = createResidue CIO > add r i > CIO = createUnit CIO > add CIO r > saveOff CIO ./ions94.lib Saving CIO. Building topology. Building atom parameters. > > i = createAtom Na+ IP 1.0 > set i element Na > set i position { 0 0 0 } > r = createResidue Na+ > add r i > Na+ = createUnit Na+ > add Na+ r > saveOff Na+ ./ions94.lib Saving Na+. Building topology. Building atom parameters. > > i = createAtom K+ K 1.0 > set i element K > set i position { 0 0 0 } > r = createResidue K+ > add r i > K+ = createUnit K+ > add K+ r > saveOff K+ ./ions94.lib Saving K+. Building topology. Building atom parameters. > > i = createAtom Rb+ Rb 1.0 > set i element Rb > set i position { 0 0 0 } > r = createResidue Rb+ > add r i > Rb+ = createUnit Rb+ > add Rb+ r > saveOff Rb+ ./ions94.lib Saving Rb+. Building topology. Building atom parameters. > > i = createAtom Cs+ Cs 1.0 > set i element Cs > set i position { 0 0 0 } > r = createResidue Cs+ > add r i > Cs+ = createUnit Cs+ > add Cs+ r > saveOff Cs+ ./ions94.lib Saving Cs+. Building topology. Building atom parameters. > > i = createAtom Cl- IM -1.0 > set i element Cl > set i position { 0 0 0 } > r = createResidue Cl- > add r i > Cl- = createUnit Cl- > add Cl- r > saveOff Cl- ./ions94.lib Saving Cl-. Building topology. Building atom parameters. > > i = createAtom MG MG 2.0 > set i element Mg > set i position { 0 0 0 } > r = createResidue MG2 > add r i > MG2 = createUnit MG2 > add MG2 r > saveOff MG2 ./ions94.lib Saving MG2. Building topology. Building atom parameters. > > i = createAtom IB IB 1.0 > set i element Cs > set i position { 0 0 0 } > r = createResidue IB > add r i > IB = createUnit IB > add IB r > saveOff IB ./ions94.lib Saving IB. Building topology. Building atom parameters. > quit Quit