! ! xplor-nih protein parameter file, version 2.0 ! ! This file is intended to work with the topology file protein-2.0.top ! ! This is a re-named copy of the file parallhdg_procheck.pro ! ! We've created this new filename in order to eliminate confusion ! between the various parameter/topology combinations that ship ! with xplor-nih. It has version numbers, and will be updated ! along with the rest of the xplor-nih package. ! ! Its backbone bond lengths and angles are designed to agree with ! the Engh & Huber parameter set (reference below), which is used by ! PROCHECK, among other structure-validation programs. ! ! If you find errors, PLEASE let us know. ! remark file protein-1.0.par remark Changed version of parallhdg_new.pro so that the bond lengths and angles remark agree with what PROCHECK expects. remark JJK 9/14/98 ! file parallhdg_new.pro ! geometric energy function parameters for distance geometry and ! simulated annealing. Modified by G.M.C. to have sigma's of Param19x and parafloat set message off echo off end ! The values of the force constants are somewhat arbitrary. The aim ! is to make ALL of them stiff compared to the weight on the NOE ! term. The force constant for the angles is adjusted such that the ! 1-3 distance is approximately as well maintained as the 1-2 distance. ! ! All angles around tetrahedral carbons (type CT) have been set ! to the ideal methane value, 109.5 degrees, by JK. ! ! the non-bonded parameters have been modified such that they ! give approximately the large DISMAN radii with repel=0.9, ! and the small DISMAN radii (or the DISGEO radii) with ! repel= 0.75. ! remark corrected proline angles to Engh & Huber, Acta Cryst., A47, 392 (1991) values. remark Needed to define a new atom type, CP, which is equivalent to their remark CH2P atom type. JJK 9/22/95 ! {* set energy constants *} evaluate ($kbon = 1000) ! kcal / mol-A^2 evaluate ($kang = 500) ! kcal / mol-rad^2 evaluate ($kchi = 500) ! kcal / mol-rad^2 evaluate ($kback = 500) evaluate ($kpx = $kback) if ( $exist_weak_omega = TRUE ) then if ( $weak_omega=1 ) then evaluate ($kpx = $kback*0.5) display reducing the omega improper force constant end if end if evaluate ($kssbon = 1000) evaluate ($kssang = 500) evaluate ($kpla = 500) ! kcal / mol-rad^2 evaluate ($kdih = 0) ! kcal / mol-rad^2 if ( $exist_use_dihe = TRUE ) then if ( $use_dihe=1 ) then evaluate ($kdih = 50) ! kcal / mol-rad^2 display enabling the dihe force constant end if end if ! BONDS bonds H NA $kbon 0.98 bonds H NB $kbon 0.98 ! protonated his, copied from his ND-HD bond JJK 7/2/99 bond H NH2 $kbon 0.98 bond H NH1 $kbon 0.98 bond H OH $kbon 0.96 bond H S $kbon 0.96 bond HA CT $kbon 1.08 bond HA CP $kbon 1.08 ! CP added bond HA C $kbon 1.08 bond HC NC2 $kbon 1.00 bond HC NH1 $kbon 0.98 bond HC NH3 $kbon 1.04 bond C C $kbon 1.38 bond C CT $kbon 1.525 ! was 1.530 PROCHECK bond C N $kbon 1.305 bond C NP $kbon 1.305 bond C NR $kbon 1.305 bond C NH1 $kbon 1.329 ! was 1.305 PROCHECK bond C NH2 $kbon 1.305 bond C NC2 $kbon 1.305 bond C O $kbon 1.231 ! was 1.215 PROCHECK bond C OC $kbon 1.22 bond C OH $kbon 1.38 bond C CA $kbon 1.400 bond CA CA $kbon 1.400 bond CA CB $kbon 1.404 bond CA CN $kbon 1.400 bond CA CT $kbon 1.510 bond CA HA $kbon 1.080 bond CB CN $kbon 1.419 bond CC CT $kbon 1.504 bond CC CV $kbon 1.375 bond CC NA $kbon 1.385 bond CN NA $kbon 1.380 bond CR HA $kbon 1.080 bond CR NA $kbon 1.343 bond CR NB $kbon 1.3350 bond CT CT $kbon 1.53 bond CP CP $kbon 1.53 bond CP CT $kbon 1.492 ! CP bond CT N $kbon 1.49 bond CP N $kbon 1.473 ! CP bond CP NH3 $kbon 1.49 ! CP - proline at N terminus bond CT NH1 $kbon 1.458 ! was 1.490 PROCHECK bond CT NH2 $kbon 1.49 bond CT NH3 $kbon 1.49 bond CT NC2 $kbon 1.49 bond CT OH $kbon 1.42 bond CT S $kbon 1.81 bond CV HA $kbon 1.080 bond CV NB $kbon 1.394 bond CX CB $kbon 1.459 bond CX CT $kbon 1.495 bond CX CW $kbon 1.352 bond CW HA $kbon 1.080 bond CW NA $kbon 1.381 bond S S $kssbon 2.02 ! ANGLES angle H NH1 H $kang 107.5 angle H NH1 C $kang 120.0 angle H NH1 CT $kang 120.0 angle H NH2 H $kang 120.0 angle H NH2 C $kang 120.0 angle H NH2 CT $kang 120.0 angle H OH CT $kang 108.0 angle H S CT $kang 108.0 angle H OH C $kang 108.0 angle HC NH3 HC $kang 109.5 angle HC NH3 CT $kang 109.5 angle HC NH3 CP $kang 109.5 ! CP, in N-terminal pro angle HC NC2 HC $kang 120.0 angle HC NC2 C $kang 120.0 angle HC NC2 CT $kang 107.5 angle HA C C $kang 120.0 angle HA C NH1 $kang 120.0 angle HA C NH2 $kang 120.0 angle HA C NR $kang 120.0 angle HA C O $kang 120.0 angle HA CR NA $kang 124.2 !corrected by JK angle HA CR NB $kang 124.2 !corrected by JK angle HA CT HA $kang 109.5 angle HA CT C $kang 109.5 angle HA CT CT $kang 109.5 angle HA CT N $kang 109.5 angle HA CT NH1 $kang 109.5 angle HA CT NH3 $kang 109.5 angle HA CT NC2 $kang 109.5 angle HA CT OH $kang 109.5 !corrected by JK angle HA CT S $kang 109.5 angle HA CV NB $kang 125.05 !corrected by JK angle HA CW NA $kang 125.65 !corrected JK angle HA CT CP $kang 109.5 ! CP hydrogen angles are guesses angle HA CP CT $kang 109.5 ! CP angle HA CP HA $kang 109.5 ! CP angle HA CP CP $kang 109.5 ! CP angle HA CP N $kang 109.5 ! CP angle HA CP NH3 $kang 109.5 ! CP, N-terminal pro angle C C C $kang 126.5 angle C C CT $kang 122.3 angle C C NH1 $kang 108.6 angle C C NP $kang 109.5 angle C C NR $kang 109.5 angle C C OH $kang 122.3 angle C CA CA $kang 120.000 angle C CA HA $kang 120.0 angle C CT CT $kang 110.10 ! was 109.5 PROCHECK angle C CT N $kang 111.8 ! updated with CP angle C CT NH1 $kang 111.2 ! was 109.5 PROCHECK angle C CT NH2 $kang 109.5 angle C CT NH3 $kang 109.5 angle C N CT $kang 122.6 ! updated with CP angle C N CP $kang 125.0 ! CP angle C NH1 C $kang 119.1 angle C NH1 CT $kang 121.7 ! was 120.0 PROCHECK was by JK unq. ARG angle C NC2 CT $kang 107.5 angle C NP C $kang 106.0 angle C NR C $kang 106.0 angle CA C CA $kang 120.0 angle CA C OH $kang 120.0 angle CA CA CA $kang 120.0 angle CA CA CB $kang 120.0 angle CA CA CN $kang 120.0 angle CA CA CT $kang 120.0 angle CA CA HA $kang 120.000 angle CA CB CN $kang 118.0 angle CA CN CB $kang 122.0 angle CA CT CT $kang 109.5 angle CA CT HA $kang 109.5000 angle CB CA HA $kang 120.0 angle CB CX CT $kang 128.6 angle CB CX CW $kang 106.4 angle CB CN NA $kang 104.40 angle CC CT CT $kang 109.5 angle CC CT HA $kang 109.5000 angle CC CV HA $kang 125.05 !corrected by JK angle CC CV NB $kang 109.9000 angle CC NA CR $kang 107.3000 angle CC NA H $kang 126.300 angle CN CA HA $kang 120.00 angle CN NA CW $kang 111.6000 angle CN NA H $kang 123.100 angle CR NA H $kang 126.3000 angle CR NB CV $kang 105.3000 angle CV NB H $kang 127.35 ! added for protonated his, JJK 7/2/99 angle CR NB H $kang 127.35 ! added for protonated his, JJK 7/2/99 angle CT C N $kang 116.9 ! updated with CP angle CT C NH1 $kang 116.2 ! was 117.5 PROCHECK angle CT C NH2 $kang 120.0 angle CT C O $kang 120.80 ! was 121.25 PROCHECK was by JK (pept planarity) angle CT C OH $kang 117.5 angle CT C OC $kang 118.0 angle CT CC CV $kang 131.900 angle CT CC NA $kang 122.2000 angle CT CT CT $kang 109.5 !JK angle CT CT N $kang 103.0 ! updated with CP angle CP CP N $kang 103.2 ! CP angle CP CP NH3 $kang 103.2 ! CP, N-terminal pro angle CP CP CT $kang 106.1 ! CP angle CP CT CT $kang 104.5 ! CP angle CT CT NH1 $kang 110.5 ! was 109.5 PROCHECK angle CT CT NH2 $kang 109.5 angle CT CT NH3 $kang 109.5 angle CT CT NC2 $kang 109.5 angle CT CT OH $kang 109.5 !corrected by JK angle CT CT S $kang 109.5 angle CT CX CW $kang 125.0000 angle CT N CT $kang 119.5 !PRO angle CT N CP $kang 112.0 ! CP angle CT NH3 CP $kang 109.5 ! CP, N-terminal pro angle CT NH3 CT $kang 109.5 !PRO N-ter angle CT S CT $kang 97.20 angle CT S S $kssang 104.2 angle CV CC NA $kang 105.900 angle CW NA H $kang 125.300 angle CX CB CN $kang 108.800 angle CX CT CT $kang 109.5 angle CX CT HA $kang 109.5 angle CX CW HA $kang 125.65 !corrected by JK angle CX CW NA $kang 108.7 angle N C O $kang 122.0 ! updated with CP angle NA CR NB $kang 111.60 angle NH1 C NC2 $kang 120.0 !corrected by JK angle NH1 C NR $kang 117.0 angle NH1 C O $kang 123.00 ! was 121.25 PROCHECK was by JK (pept planarity) angle NH2 C O $kang 120.6 angle NC2 C NC2 $kang 120.0 !corrected by JK angle O C OH $kang 124.5 angle OC C OC $kang 124.0 !corrected by JK angle CA CN NA $kang 133.6 !trp addition angle CA CB CX $kang 133.2 !trp addition ! IMPROPERS ! For dihedrals and impropers, the following convention was adopted: ! All dihedral terms maintaining planarity (esp. omega) have been ! converted into impropers. The only dihedrals left are around ! rotatable bonds. improper H X X C $kpla 0 0.0 improper H X X NH1 $kpla 0 0.0 improper H X X NH2 $kpla 0 0.0 improper H X X O $kpla 0 0.0 improper HC X X NH1 $kpla 0 0.0 improper HC X X NC2 $kpla 0 0.0 improper HC X X NH3 $kpla 0 0.0 improper HA X X C $kpla 0 0.0 improper C X X C $kpla 0 0.0 improper C X X CT $kpla 0 0.0 improper C X X N $kpla 0 0.0 improper C X X NH1 $kpla 0 0.0 improper C X X NH2 $kpla 0 0.0 improper C X X NC2 $kpla 0 0.0 improper C X X NR $kpla 0 0.0 improper C X X O $kpla 0 0.0 improper C X X OH $kpla 0 0.0 improper C X X OC $kpla 0 0.0 improper CT X X N $kpla 0 0.0 improper CP CT CT N $kpla 0 0.0 ! new pro ring pucker --JK improper CP CT CT NH3 $kpla 0 0.0 ! CP, N-terminal pro improper CT X X NH1 $kpla 0 0.0 improper CT X X NH3 $kpla 0 0.0 improper CT X X NC2 $kpla 0 0.0 improper CT X X NR $kpla 0 0.0 improper NH1 X X NH1 $kpla 0 0.0 improper NH1 X X NR $kpla 0 0.0 improper NH1 CT NC2 HC $kpla 0 0.0 ! Arg improper CT C NH2 H $kpla 0 0.0 ! Asn and Gln ! note the way the omega planarity is defined which allows switch ! between trans and cis by a patch. improper CT C NH1 CT $kpx 0 180.0 ! new trans peptide bond improper CT C N CT $kback 0 180.0 ! proline improper CT N C CP $kback 0 180.0 ! CP peptide bond improper CT N CP C $kback 0 180.0 ! CP cis peptide bond improper O C NH1 CT $kpx 0 0.0 ! CO peptide planarity improper O C N CT $kback 0 0.0 ! proline improper H NH1 C CT $kpx 0 0.0 ! NH peptide planarity improper C CT CT NH1 $kpx 0 180.0 ! trans peptide bond improper C CT NH1 CT $kback 0 180.0 ! cis peptide bond improper C CT CT N $kback 0 180.0 ! Pro trans peptide bond improper C CT N CT $kback 0 180.0 ! Pro cis peptide bond ! 65.977 degrees for the chirality restraints are from ! isolated CAs minimized with bonds and angles only --JK improper HA NH1 C CT $kchi 0 65.977 ! CA chirality improper HA N C CT $kchi 0 65.977 ! Pro CA chirality improper HA NH3 C CT $kchi 0 65.977 ! N-terminal CA chirality improper HA C NH1 CT $kchi 0 65.977 ! D CA chirality improper HA C N CT $kchi 0 65.977 ! D Pro CA chirality improper HA C NH3 CT $kchi 0 65.977 ! D N-terminal CA chirality improper HA CT OH CT $kchi 0 65.977 ! Thr CB chirality improper HA CT CT CT $kchi 0 -65.977 ! val, leu, ile CB chirality ! stereospecific hydrogen impropers improper HA HA NH1 C $kchi 0 -70.874 ! stereo GLY CA improper HA HA NH3 C $kchi 0 -70.874 ! stereo N-terminal GLY CA JJK 8/16/02 improper HA HA CT HA $kchi 0 -66.514 ! methyl improper HA HA S HA $kchi 0 -66.0 ! met methyl improper HC HC CT HC $kchi 0 -66.0 ! amine for lys & N terminus improper HC HC CT CT $kchi 0 -70.874 ! PRO N-terminus improper HC HC CT CP $kchi 0 -70.874 ! CP, N-terminal pro improper HA HA CT CT $kchi 0 -70.874 ! methylene ! need to get better values for this improper HA HA CT CP $kchi 0 -70.874 ! CP methylene improper HA HA CP N $kchi 0 -70.874 ! CP methylene improper HA HA CP NH3 $kchi 0 -70.874 ! CP methylene N-terminal improper HA HA CT CA $kchi 0 -70.874 ! methylene phe improper HA HA CT CX $kchi 0 -70.874 ! methylene trp improper HA HA CT CC $kchi 0 -70.874 ! methylene his improper HA HA CT C $kchi 0 -70.874 ! methylene glu, asp improper HA HA C NH1 $kchi 0 -70.874 ! methylene gly improper HA HA CT NH1 $kchi 0 -70.874 ! methylene arg improper HA HA CT NH3 $kchi 0 -70.874 ! methylene lys improper HA HA CT N $kchi 0 -70.874 ! methylene pro improper HA HA CT S $kchi 0 -73.230 ! methylene cys, met improper HA HA CT OH $kchi 0 -71.884 ! methylene ser ! hold rings flat (from parallhgeo) ! trp improper CB CN CA CA $kpla 0 0.0 improper CN CA CA CA $kpla 0 0.0 improper CA CA CA CA $kpla 0 0.0 improper CA CA CA CB $kpla 0 0.0 improper CA CA CB CN $kpla 0 0.0 improper CA CB CN CA $kpla 0 0.0 improper CW NA CN CA $kpla 0 180.0 improper CW CX CB CA $kpla 0 180.0 improper NA CN CA CA $kpla 0 180.0 improper NA CN CB CA $kpla 0 180.0 improper CX CB CA CA $kpla 0 180.0 improper CX CB CN CA $kpla 0 180.0 improper HA CA CA CA $kpla 0 180.0 improper H NA CN CB $kpla 0 180.0 improper HA CW NA CN $kpla 0 180.0 improper CT CX CB CN $kpla 0 180.0 !phe improper CT CA CA CA $kpla 0 180.0 !tyr improper OH C CA CA $kpla 0 180.0 improper HA CA CA C $kpla 0 180.0 improper HA CA C CA $kpla 0 180.0 ! improper CA C CA HA $kpla 0 0.0 improper CA CA C CA $kpla 0 0.0 improper CA CA C HA $kpla 0 0.0 improper CA CA CA C $kpla 0 0.0 improper CA CA CB HA $kpla 0 0.0 improper CA CA CN CA $kpla 0 0.0 improper CA CB CA CA $kpla 0 0.0 improper CA CN CA HA $kpla 0 0.0 improper CB CX CN CA $kpla 0 0.0 improper CC CT NA CV $kpla 0 0.0 improper CC NA CR NB $kpla 0 0.0 improper CN CB CA NA $kpla 0 0.0 improper CN CB CX CW $kpla 0 0.0 improper CN NA CW CX $kpla 0 0.0 improper CR NA NB HA $kpla 0 0.0 improper CR NB CV CC $kpla 0 0.0 improper CV CC NA CR $kpla 0 0.0 improper CV NB CC HA $kpla 0 0.0 improper CW CX NA HA $kpla 0 0.0 improper CW NA CN CB $kpla 0 0.0 improper CX CW CB CT $kpla 0 0.0 improper NA CN CB CX $kpla 0 0.0 improper NA CR CC H $kpla 0 0.0 improper NA CR NB CV $kpla 0 0.0 improper NA CW CN H $kpla 0 0.0 improper NA CW CX CB $kpla 0 0.0 improper NB CV CC NA $kpla 0 0.0 improper NB CV CR H $kpla 0 0.0 ! DIHEDRALS dihedral CA CA CT CT $kdih 3 0.0 dihedral CW CX CT CT $kdih 3 0.0 dihedral NA CC CT CT $kdih 3 0.0 dihedral X NH1 CT X $kdih 3 0.0 ! chi1 - chi4 dihedral X CT CT X $kdih 3 0.0 ! chi1 - chi4 dihedral X C CT X $kdih 3 0.0 ! chi1 - chi4 dihedral X S CT X $kdih 3 0.0 ! chi1 - chi4 !Radii as in CHARMM param19x ! the radius is sigma*2^(-5/6) ! use repel of 0.80 ! eps sigma eps(1:4) sigma(1:4) ! nonbonded C 0.0903 3.2072 0.0903 3.2072 ! NONBonded CA 0.120 3.2072 0.120 3.2072 NONBonded CB 0.145 3.2072 0.145 3.2072 NONBonded CC 0.145 3.2072 0.145 3.2072 NONBonded CN 0.145 3.2072 0.145 3.2072 NONBonded CR 0.1200 3.2072 0.1200 3.2072 nonbonded CT 0.0903 3.2072 0.0903 3.2072 nonbonded CP 0.0903 3.2072 0.0903 3.2072 ! CP NONBonded CV 0.1200 3.2072 0.1200 3.2072 NONBonded CW 0.1200 3.2072 0.1200 3.2072 NONBonded CX 0.1450 3.2072 0.1450 3.2072 nonbonded H 0.0498 1.4254 0.0498 1.4254 ! nonbonded HA 0.0045 2.6157 0.0045 2.6157 nonbonded HC 0.0498 1.4254 0.0498 1.4254 nonbonded N 0.1592 2.7618 0.1592 2.7618 ! NONBonded NA 0.1592 2.7618 0.1592 2.7618 NONBonded NB 0.1592 2.7618 0.1592 2.7618 nonbonded NC2 0.1592 2.7618 0.1592 2.7618 nonbonded NH1 0.1592 2.7618 0.1592 2.7618 nonbonded NH2 0.1592 2.7618 0.1592 2.7618 nonbonded NH3 0.1592 2.7618 0.1592 2.7618 nonbonded O 0.2342 2.6406 0.2342 2.6406 ! nonbonded OC 1.0244 2.6406 1.0244 2.6406 nonbonded OH 0.2342 2.6406 0.2342 2.6406 nonbonded S 0.0239 3.3854 0.0239 3.3854 ! ! the following nbfixes allow hydrogen bonding ! the distance used is (2A/B)^(1/6)*repel distances ! A B A1-4 B1-4 nbfix H NB 44.2 1.0 44.2 1.0 ! 2.111 1.900 1.689 1.583 nbfix H O 44.2 1.0 44.2 1.0 nbfix H OC 44.2 1.0 44.2 1.0 nbfix H OH 44.2 1.0 44.2 1.0 nbfix HC NB 44.2 1.0 44.2 1.0 nbfix HC O 44.2 1.0 44.2 1.0 nbfix HC OC 44.2 1.0 44.2 1.0 nbfix HC OH 44.2 1.0 44.2 1.0 ! extra parameters for phosphoserine and phosphocysteine ! these should probably be placed elsewhere ! CDS 2005/7/6 ! evaluate ($ktran=500.0) evaluate ($ktran2 = $ktran/2) evaluate ($ktran25 = $ktran/2.5) bond PPP OH 500.0 2.0 !20.0 3.3 angle OH PPP OP1 $ktran2 109.0 angle OH PPP OP2 $ktran2 109.0 angle OH PPP OP3 $ktran2 109.0 angle CT OH PPP $ktran25 97.0 angle C OH PPP $ktran25 97.0 !is this right? bond PPP S 500.0 2.0 !20.0 3.3 angle S PPP OP1 $ktran2 109.0 angle S PPP OP2 $ktran2 109.0 angle S PPP OP3 $ktran2 109.0 angle CT S PPP $ktran25 97.0 set message $prev_messages echo $prev_echo end