remark - parameter file PROLSQ.PRO - remark Trying to match PROLSQ energy functions - ak set echo=false end !! PROLSQ uses a standard deviation for energy parameters !! in general the form is (1 / sigma ^ 2) !! so k-factors are calculated to match these standard deviations: !! Bond Length sigma = .02 A !! Angle-related distance sigma = .03 A !! Planar groups sigma = .02 A !! Chiral centers sigma = .15 A !! Planar peptide w torsion angle sigma = 3 degrees !! For the non-bonded energy term, the function is of the form !! (1 / sigma ^ 4) !! Nonbonded interactions sigma = .5 A evaluate ( $kbond = 2500.0 ) !dimension: ( kcal / mole-A^2 ) evaluate ( $kangle = 584.0 ) !dimension: ( kcal / mole-rad^2 ) evaluate ( $omega = 1700.0 ) !dimension: ( kcal / mole ) evaluate ( $pro_omega = 100.0 ) !dimension: ( kcal / mole ) evaluate ( $plane = 360.0 ) !dimension: ( kcal / mole-rad^2 ) evaluate ( $chiral = 796.0 ) !dimension: ( kcal / mole-rad^2 ) !! All bond paramaters are set to 2500.0 to match a standard deviation of !! sigma = .02 in PROLSQ bond C C $kbond 1.38 bond C CH1E $kbond 1.52 bond C CH2E $kbond 1.52 bond C CH3E $kbond 1.52 bond C CR1E $kbond 1.38 bond C N $kbond 1.33 bond C NC2 $kbond 1.33 bond C NH1 $kbond 1.33 bond C NH2 $kbond 1.33 bond C NP $kbond 1.33 bond C NR $kbond 1.33 bond C O $kbond 1.23 bond C OC $kbond 1.23 bond C OH1 $kbond 1.38 bond C OS $kbond 1.43 bond CH1E CH1E $kbond 1.53 bond CH1E CH2E $kbond 1.52 bond CH1E CH3E $kbond 1.52 bond CH1E N $kbond 1.45 bond CH1E NH1 $kbond 1.45 bond CH1E NH2 $kbond 1.45 bond CH1E NH3 $kbond 1.45 bond CH1E OH1 $kbond 1.42 bond CH2E CH2E $kbond 1.52 bond CH2E CH3E $kbond 1.54 bond CH2E CR1E $kbond 1.45 bond CH2E N $kbond 1.45 bond CH2E NH1 $kbond 1.45 bond CH2E NH2 $kbond 1.45 bond CH2E NH3 $kbond 1.45 bond CH2E OH1 $kbond 1.42 bond CH2E S $kbond 1.81 bond CH2E SH1E $kbond 1.81 bond CH3E NH1 $kbond 1.49 bond CH3E NR $kbond 1.49 bond CH3E S $kbond 1.77 bond CH3E OS $kbond 1.38 bond CM OM $kbond 1.128 bond CR1E CR1E $kbond 1.38 bond CR1E NH1 $kbond 1.305 bond CR1E NR $kbond 1.305 bond H NH1 $kbond 0.98 bond H NH2 $kbond 0.98 bond H OH1 $kbond 0.96 bond HA C $kbond 1.08 bond HC NC2 $kbond 1.00 bond HC NH1 $kbond 0.98 bond HC NH3 $kbond 1.04 bond OC S $kbond 1.43 bond OM OM $kbond 1.23 bond S S $kbond 2.02 !! The energy parameter for angles was determinded by taking an ideal !! situation of two bonds of length 1.45 A and an angle of 120 degrees !! and letting it deviate by 1.5 degrees in either direction and !! taking the average of the two directions. angle C C C $kangle 106.5 angle C C CH2E $kangle 126.5 angle C C CH3E $kangle 126.5 angle C C CR1E $kangle 122.5 angle C C HA $kangle 120.0 angle C C NH1 $kangle 109.0 angle C C NP $kangle 112.5 angle C C NR $kangle 112.5 angle C C OH1 $kangle 119.0 angle C C O $kangle 119.0 angle CH1E C N $kangle 117.5 angle CH1E C NH1 $kangle 117.5 angle CH1E C O $kangle 121.5 angle CH1E C OC $kangle 117.5 angle CH1E C OH1 $kangle 120.0 angle CH2E C CR1E $kangle 121.5 angle CH2E C N $kangle 117.5 angle CH2E C NH1 $kangle 117.5 angle CH2E C NH2 $kangle 117.5 angle CH2E C NC2 $kangle 117.5 angle CH2E C NR $kangle 116.0 angle CH2E C O $kangle 121.6 angle CH2E C OC $kangle 118.5 angle CH2E C OH1 $kangle 120.0 angle CH3E C N $kangle 117.5 angle CH3E C NH1 $kangle 117.5 angle CH3E C O $kangle 121.5 angle CR1E C CR1E $kangle 120.5 angle CR1E C NH1 $kangle 110.5 angle CR1E C NP $kangle 122.5 angle CR1E C NR $kangle 122.5 angle CR1E C OH1 $kangle 119.0 angle N C O $kangle 121.0 angle NC2 C NC2 $kangle 120.0 angle NC2 C NH1 $kangle 120.0 angle NH1 C NR $kangle 120.0 angle NH1 C O $kangle 121.0 angle NH2 C O $kangle 121.0 angle O C OH1 $kangle 120.0 angle OC C OC $kangle 122.5 angle OS C CH1E $kangle 125.3 angle OS C CH2E $kangle 125.3 angle OS C O $kangle 120.0 angle C CH1E CH1E $kangle 110.0 angle C CH1E CH2E $kangle 109.5 angle C CH1E CH3E $kangle 106.5 angle C CH1E N $kangle 111.6 angle C CH1E NH1 $kangle 111.6 angle C CH1E NH2 $kangle 111.6 angle C CH1E NH3 $kangle 111.6 angle CH1E CH1E CH2E $kangle 112.5 angle CH1E CH1E CH3E $kangle 111.0 angle CH1E CH1E NH1 $kangle 110.0 angle CH1E CH1E NH2 $kangle 109.5 angle CH1E CH1E NH3 $kangle 107.5 angle CH1E CH1E OH1 $kangle 104.5 angle CH2E CH1E CH3E $kangle 111.5 angle CH2E CH1E N $kangle 104.0 angle CH2E CH1E NH1 $kangle 110.0 angle CH2E CH1E NH2 $kangle 110.0 angle CH2E CH1E NH3 $kangle 110.0 angle CH3E CH1E CH3E $kangle 111.0 angle CH3E CH1E NH1 $kangle 108.5 angle CH3E CH1E NH2 $kangle 109.5 angle CH3E CH1E NH3 $kangle 109.5 angle CH3E CH1E OH1 $kangle 110.5 angle C CH2E CH1E $kangle 112.5 angle C CH2E CH2E $kangle 113.0 angle C CH2E NH1 $kangle 111.6 angle C CH2E NH2 $kangle 111.6 angle C CH2E NH3 $kangle 111.6 angle CH1E CH2E CH1E $kangle 117.0 angle CH1E CH2E CH2E $kangle 112.5 angle CH1E CH2E CH3E $kangle 113.0 angle CH1E CH2E OH1 $kangle 111.0 angle CH3E CH2E OH1 $kangle 111.0 angle CH1E CH2E S $kangle 112.5 angle CH1E CH2E SH1E $kangle 112.5 angle CH2E CH2E CH2E $kangle 110.0 angle CH2E CH2E CH3E $kangle 111.0 angle CH2E CH2E N $kangle 105.0 angle CH2E CH2E NH1 $kangle 111.0 angle CH2E CH2E NH2 $kangle 109.5 angle CH2E CH2E NH3 $kangle 110.5 angle CH2E CH2E S $kangle 112.5 angle C CR1E C $kangle 126.5 angle C CR1E CH2E $kangle 122.0 angle C CR1E CR1E $kangle 119.0 angle C CR1E NH1 $kangle 109.5 angle C CR1E NR $kangle 106.5 angle CR1E CR1E CR1E $kangle 120.5 angle NH1 CR1E NH1 $kangle 109.0 angle NH1 CR1E NR $kangle 109.0 angle C N CH1E $kangle 120.0 angle C N CH2E $kangle 120.0 angle C N CT $kangle 120.0 angle CH1E N CH2E $kangle 110.0 angle CH1E N CH3E $kangle 110.0 angle CH2E N CH3E $kangle 109.5 angle CT N CT $kangle 110.0 angle C NC2 CT $kangle 120.0 angle C NC2 HC $kangle 120.0 angle HC NC2 HC $kangle 120.0 angle C NH1 C $kangle 102.5 angle C NH1 CH1E $kangle 120.0 angle C NH1 CH2E $kangle 120.0 angle C NH1 CH3E $kangle 120.0 angle C NH1 CR1E $kangle 108.0 angle C NH1 H $kangle 120.0 angle CH1E NH1 CH3E $kangle 120.0 angle CH1E NH1 H $kangle 120.0 angle CH2E NH1 CH3E $kangle 120.0 angle CH2E NH1 H $kangle 120.0 angle CH3E NH1 H $kangle 120.0 angle CR1E NH1 CR1E $kangle 110.0 angle CR1E NH1 H $kangle 120.0 angle C NH2 H $kangle 120.0 angle CH1E NH2 CH2E $kangle 120.0 angle CH1E NH2 H $kangle 120.0 angle CH2E NH2 H $kangle 120.0 angle H NH2 H $kangle 125.0 angle C NP C $kangle 102.5 angle C NR C $kangle 102.5 angle C NR CR1E $kangle 109.5 angle CH3E NR CR1E $kangle 109.5 angle CH3E NR C $kangle 109.5 angle CR1E NR CR1E $kangle 110.0 angle CH1E NH3 HC $kangle 109.5 angle CH1E NH3 CH2E $kangle 109.5 angle CH2E NH3 HC $kangle 109.5 angle HC NH3 HC $kangle 109.5 angle C OH1 H $kangle 109.5 angle CH1E OH1 H $kangle 109.5 angle CH2E OH1 H $kangle 109.5 angle C OS CH3E $kangle 120.5 angle CH2E S CH3E $kangle 99.5 angle CH2E S S $kangle 104.2 angle OC S OC $kangle 109.5 !! The only dihedral term that is not being set to zero is the term that !! preserves planarity of the peptide bond. The constant came from a !! comparison of the strength of the two different energy functions under !! small deviations. dihe X C NH1 X $omega 1 0.0 dihe CH1E C N CH1E $pro_omega 2 180.0 dihe CH2E C N CH1E $pro_omega 2 180.0 dihe CR1E C C CR1E $pro_omega 2 180.0 !fixed, ATB dihe CR1E C C C $pro_omega 2 180.0 dihe CR1E C C NH1 $pro_omega 2 180.0 dihe X C CH1E X 0.0 3 0.0 dihe X C CH2E X 0.0 3 0.0 dihe X C CR1E X 0.0 2 180.0 dihe X C CT X 0.0 3 0.0 dihe X C N X 0.0 2 180.0 dihe X C NC2 X 0.0 2 180.0 dihe X C NH2 X 0.0 2 180.0 dihe X C OH1 X 0.0 2 180.0 dihe X C OS X 0.0 2 180.0 dihe X CH1E CH1E X 0.0 3 0.0 dihe X CH1E CH2E X 0.0 3 0.0 dihe X CH1E N X 0.0 3 0.0 dihe X CH1E NH1 X 0.0 3 0.0 dihe X CH1E NH2 X 0.0 3 0.0 dihe X CH1E NH3 X 0.0 3 0.0 dihe X CH1E OH1 X 0.0 3 0.0 dihe X CH2E CH2E X 0.0 3 0.0 dihe X CH2E N X 0.0 3 0.0 dihe X CH2E NH1 X 0.0 3 0.0 dihe X CH2E NH2 X 0.0 3 0.0 dihe X CH2E NH3 X 0.0 3 0.0 dihe X CH2E OH1 X 0.0 3 0.0 dihe X CH2E S X 0.0 2 0.0 dihe X CT CT X 0.0 3 0.0 dihe X CT N X 0.0 3 0.0 dihe X CT NC2 X 0.0 3 0.0 dihe X CT NH1 X 0.0 3 0.0 dihe X CT NH2 X 0.0 3 0.0 dihe X CT NH3 X 0.0 3 0.0 dihe X CT OH1 X 0.0 3 0.0 dihe X CT S X 0.0 2 0.0 dihe X FE NR X 0.0 4 0.0 dihe X FE CM X 0.0 4 0.0 dihe X FE OM X 0.0 4 0.0 dihe X S S X 0.0 2 0.0 !! There are only two kinds of improper terms that are not set to zero: !! the terms that preserve the planarity of the rings and the terms that !! preserve the chirality of tetrahedral atoms. The chiral constant comes !! from comparing the relative strength of the two functions when the !! chirality is completely reversed. The planarity constant comes from !! a comparison of the two functions under small deviaions from a perfect !! plane. impr C C CR1E CH2E $plane 0 0.0 impr C CR1E C CH2E $plane 0 0.0 impr C CR1E CR1E CH2E $plane 0 0.0 impr C CR1E NH1 CH2E $plane 0 0.0 impr C NH1 CR1E CH2E $plane 0 0.0 impr C CR1E CR1E OH1 $plane 0 0.0 impr C X X C $plane 0 0.0 impr C X X CH2E $plane 0 0.0 impr C X X CH3E $plane 0 0.0 impr C X X CR1E $plane 0 0.0 impr CR1E X X CR1E $plane 0 0.0 impr CR1E X X NH1 $plane 0 0.0 impr NR X X CR1E $plane 0 0.0 impr CH1E X X CH1E $chiral 0 35.26439 impr CH1E X X CH2E $chiral 0 35.26439 impr CH1E X X CH3E $chiral 0 35.26439 impr C H H NH2 0.0 0 0.0 impr C OC OC CH1E 0.0 0 0.0 impr C OC OC CH2E 0.0 0 0.0 impr C X X H 0.0 0 0.0 impr C X X HA 0.0 0 0.0 impr C X X NH1 0.0 0 0.0 impr C X X O 0.0 0 0.0 impr C X X OC 0.0 0 0.0 impr C X X OH1 0.0 0 0.0 impr H X X O 0.0 0 0.0 impr N CH1E CH2E C 0.0 0 0.0 impr N X X CH2E 0.0 0 0.0 impr N X X CT 0.0 0 0.0 impr NC2 X X CT 0.0 0 0.0 impr NC2 X X HC 0.0 0 0.0 impr NH1 X X CH1E 0.0 0 0.0 impr NH1 X X CH2E 0.0 0 0.0 impr NH1 X X CH3E 0.0 0 0.0 impr NH1 X X CT 0.0 0 0.0 impr NH1 X X H 0.0 0 0.0 impr NH1 X X NH1 0.0 0 0.0 impr NH1 X X NR 0.0 0 0.0 impr NH2 X X H 0.0 0 0.0 impr NR X X C 0.0 0 0.0 impr NR X X CT 0.0 0 0.0 impr NR X X CH3E 0.0 0 0.0 {* 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 increments Van der Waals radii for non-bonded contacts ! that involve torsion angles (1:4 contacts) by -.30 A. ! This accounts for the difference between the sigma values for ! regular contacts and (1:4) contacts. NBONds CUTNB=5.0 EPS=1.0 E14FAC=0.4 WMIN=1.5 REPEl = 1.0 ! turns on the repel function REXPonent = 4 IREXponent = 1 RCONst = 16.0 TOLErance = 0.5 NBXMOD = 5 END ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) ! --------------------------------------- NONBonded H 0.1000 2.1381 0.1000 1.8709 NONBonded HC 0.1000 2.1381 0.1000 1.8709 ! NONBonded C 0.1000 3.0291 0.1000 2.7618 NONBonded CH1E 0.1000 3.2963 0.1000 3.0291 NONBonded CH2E 0.1000 3.2963 0.1000 3.0291 NONBonded CH3E 0.1000 3.2963 0.1000 3.0291 NONBonded CR1E 0.1000 3.2963 0.1000 3.0291 ! NONBonded N 0.1000 2.7618 0.1000 2.4945 NONBonded NC2 0.1000 2.7618 0.1000 2.4945 NONBonded NH1 0.1000 2.7618 0.1000 2.4945 NONBonded NH2 0.1000 2.7618 0.1000 2.4945 NONBonded NH3 0.1000 2.7618 0.1000 2.4945 NONBonded NP 0.1000 2.7618 0.1000 2.4945 NONBonded NR 0.1000 2.7618 0.1000 2.4945 ! NONBonded O 0.1000 2.6727 0.1000 2.4054 NONBonded OC 0.1000 2.6727 0.1000 2.4054 NONBonded OH1 0.1000 2.6727 0.1000 2.4054 ! NONBonded S 0.1000 3.2072 0.1000 2.9400 NONBonded SH1E 0.1000 3.2072 0.1000 2.9400 ! set echo=true end