elseif ($par_nonbonded eq "PROLSQ") then {* nonbonding parameter section *} {* ============================ *} !! ! This uses a new form of the REPEL function: ! fVDW(R) = RCON *( Rmin ^ IREX - R ^ IREX ) ^ REXP ! ! PROLSQ uses a function of the form: ! fVDW(R) = (1 / 0.5) ^ 4 * ( Rmin ^ 4 - R ^ 4 ) ! ! The epsilon values are arbitrary since the repel function does not depend ! on epsilon. The sigma values come from converting the Van der Waals ! radii of the PROLSQ program into sigma values using the formula: ! Rmin = sigma * 2 ^ (1/6) ! Note: Prolsq decrements Van der Waals radii for non-bonded contacts ! that involve torsion angles (1:4 contacts) by .30 A, and ! hydrogen bonds (X...Y) by .2 A (X-H...Y) by .9. The former ! decrement is accomplished in CNS by using the ! 1-4 nonbonded terms. The latter decrement is accomplished by ! decreasing the van der Waals radius of hydrogens by 0.8 ! and that of O and N by 0.1 A. ! { suggested values: NBONds CUTNB=7.0 WMIN=1.5 REPEl = 1.0 REXPonent = 4 IREXponent = 1 RCONst = 16.0 TOLErance = 0.5 NBXMOD = 5 ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} END } evaluate ($repel_radius = 1.0) evaluate ($repel_rcons = 25) evaluate ($repel_rexpo = 4) evaluate ($repel_irexp = 1) ! type van der Waals radius correction applied for hbond evaluate ($VR_C= 3.7) evaluate ($VR_N= 3.0) {-0.1} evaluate ($VR_O= 2.9) {-0.1} evaluate ($VR_S= 3.6) evaluate ($VR_FE= 2.4) evaluate ($VR_H= 1.6) {from 2.4 MN} evaluate ($VR_HH= 1.6) {-0.8} evaluate ($VR_P= 3.8) evaluate ($VR_I= 4.3) evaluate ($VR_C_SP2= 3.4) { convert radii into sigmas } evaluate ($VR_C = $VR_C / 2^(1/6)) evaluate ($VR_N = $VR_N / 2^(1/6)) evaluate ($VR_O = $VR_O / 2^(1/6)) evaluate ($VR_S = $VR_S / 2^(1/6)) evaluate ($VR_FE = $VR_FE / 2^(1/6)) evaluate ($VR_H = $VR_H / 2^(1/6)) evaluate ($VR_HH = $VR_HH / 2^(1/6)) evaluate ($VR_P = $VR_P / 2^(1/6)) evaluate ($VR_I = $VR_I / 2^(1/6)) evaluate ($VR_C_SP2=$VR_C_SP2/ 2^(1/6)) { compute 1-4 sigmas } evaluate ($VR14_C = $VR_C -0.3/ 2^(1/6)) evaluate ($VR14_N = $VR_N -0.3/ 2^(1/6)) evaluate ($VR14_O = $VR_O -0.3/ 2^(1/6)) evaluate ($VR14_S = $VR_S -0.3/ 2^(1/6)) evaluate ($VR14_FE = $VR_FE -0.3/ 2^(1/6)) evaluate ($VR14_H = $VR_H -0.3/ 2^(1/6)) evaluate ($VR14_HH = $VR_HH -0.3/ 2^(1/6)) evaluate ($VR14_P = $VR_P -0.3/ 2^(1/6)) evaluate ($VR14_I = $VR_I -0.3/ 2^(1/6)) evaluate ($VR14_C_SP2=$VR_C_SP2-0.3/ 2^(1/6)) evaluate ($VE=0.1) ! ! sigma= vdw radius / 2 ^ (1/6) ! ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) (kcal/mol) (A) ! -------------------------------------------------- NONBonded H $VE $VR_HH $VE $VR14_HH NONBonded HA $VE $VR_H $VE $VR14_H ! aliphatic hydrogen NONBonded HC $VE $VR_HH $VE $VR14_HH ! h attached to charg. ! NONBonded C $VE $VR_C_SP2 $VE $VR14_C_SP2 ! carbonyl carbon NONBonded CCIS $VE $VR_C_SP2 $VE $VR14_C_SP2 ! carbonyl carbon NONBonded C5 $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded C5W $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CF $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CW $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CY $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CY2 $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CH1E $VE $VR_C $VE $VR14_C ! \ NONBonded CH2E $VE $VR_C $VE $VR14_C ! extended carbons NONBonded CH2G $VE $VR_C $VE $VR14_C ! extended carbons NONBonded CH2P $VE $VR_C $VE $VR14_C ! extended carbons NONBonded CH3E $VE $VR_C $VE $VR14_C ! / NONBonded CR1E $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CR1H $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CR1W $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CRHH $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CRH $VE $VR_C $VE $VR14_C ! ring carbons ! NONBonded N $VE $VR_N $VE $VR14_N NONBonded NC2 $VE $VR_N $VE $VR14_N NONBonded NH1 $VE $VR_N $VE $VR14_N NONBonded NH2 $VE $VR_N $VE $VR14_N NONBonded NH3 $VE $VR_N $VE $VR14_N NONBonded NP $VE $VR_N $VE $VR14_N NONBonded NR $VE $VR_N $VE $VR14_N ! NONBonded O $VE $VR_O $VE $VR14_O NONBonded OC $VE $VR_O $VE $VR14_O NONBonded OH1 $VE $VR_O $VE $VR14_O ! NONBonded S $VE $VR_S $VE $VR14_S NONBonded SM $VE $VR_S $VE $VR14_S NONBonded SH1E $VE $VR_S $VE $VR14_S