NMR Restraints Grid
| |
NMR Restraints Grid |
|
Result table
| image | mrblock_id | pdb_id | cing | in_recoord | stage | position | program | type |
|
|
16043 |
1zaq   |
cing | recoord | 1-original | 5 | XPLOR/CNS | molecular system |
remark file parallhdg.pro
remark geometric energy function parameters for distance geometry and
remark simulated annealing.
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.
!
! added planarity terms for cis bonds, VLH (7/23/92)
! added improper terms, kimpro set to 500 as a guess, VLH (7/23/92)
{* 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 ($kssbon = 1000)
evaluate ($kssang = 500)
evaluate ($kpla = 500) ! kcal / mol-rad^2
evaluate ($kdih = 0) ! kcal / mol-rad^2
evaluate ($kimpro =500)
! BONDS
bond H NA $kbon 0.98
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 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 1.53
bond C N $kbon 1.305
bond C NP $kbon 1.305
bond C NR $kbon 1.305
bond C NH1 $kbon 1.305
bond C NH2 $kbon 1.305
bond C NC2 $kbon 1.305
bond C O $kbon 1.215
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 CT N $kbon 1.49
bond CT NH1 $kbon 1.49
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 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 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 109.5
angle C CT N $kang 109.5
angle C CT NH1 $kang 109.5
angle C CT NH2 $kang 109.5
angle C CT NH3 $kang 109.5
angle C N CT $kang 119.1
angle C NH1 C $kang 119.1
angle C NH1 CT $kang 120.0 !corrected 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 CT C N $kang 115.7
angle CT C NH1 $kang 117.5
angle CT C NH2 $kang 120.0
angle CT C O $kang 121.25 !corrected 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 109.5
angle CT CT NH1 $kang 109.5
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 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 124.5
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 121.25 !corrected 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 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
improper H CH C2 OH $kimpro 0 65.0
improper H CH C2 OS $kimpro 0 65.0
! note the way the omega planarity is defined which allows switch
! between trans and cis by a patch.
improper CT C NH1 CT $kback 0 180.0 ! new trans peptide bond
improper CT C N CT $kback 0 180.0 ! proline
improper O C NH1 CT $kback 0 0.0 ! CO peptide planarity
improper O C N CT $kback 0 0.0 ! proline
improper H NH1 C CT $kback 0 0.0 ! NH peptide planarity
improper C CT CT NH1 $kback 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
! improper terms for cis CO and NH planarity, for CISP and CIPP patches
improper C O NH1 CT $kback 0 0.0 ! cis CO
improper C O N CT $kback 0 0.0 ! cis CO, proline
improper NH1 H C CT $kback 0 0.0 ! cis NH
! 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 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 HA HA CT CT $kchi 0 -70.874 ! methylene
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
! 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
! the non-bonded parameters are approximately the same as
! DISMAN's large radii for repel=0.9, and as DISMAN's small
! radii for repel=0.75. (ECEPP2)
! the epsilon values are generally not used (and should not be)
! with this force field
! the radius is sigma*2^(-5/6)
!
! eps sigma eps(1:4) sigma(1:4) repel: 1.0 0.9 0.8 0.75
! radii
nonbonded C 0.0903 3.3409 0.0903 3.3409 ! 1.875 1.688 1.5 1.406
NONBonded CA 0.120 3.3409 0.120 3.3409
NONBonded CB 0.145 3.3409 0.145 3.3409
NONBonded CC 0.145 3.3409 0.145 3.3409
NONBonded CN 0.145 3.3409 0.145 3.3409
NONBonded CR 0.1200 3.3409 0.1200 3.3409
nonbonded CT 0.0903 3.3409 0.0903 3.3409
NONBonded CV 0.1200 3.3409 0.1200 3.3409
NONBonded CW 0.1200 3.3409 0.1200 3.3409
NONBonded CX 0.1450 3.3409 0.1450 3.3409
nonbonded H 0.0498 2.2272 0.0498 2.2272 ! 1.250 1.125 1.0 0.9375
nonbonded HA 0.0045 2.2272 0.0045 2.2272
nonbonded HC 0.0498 2.2272 0.0498 2.2272
nonbonded N 0.1592 3.0068 0.1592 3.0068 ! 1.688 1.519 1.350 1.266
NONBonded NA 0.1592 3.0068 0.1592 3.0068
NONBonded NB 0.1592 3.0068 0.1592 3.0068
nonbonded NC2 0.1592 3.0068 0.1592 3.0068
nonbonded NH1 0.1592 3.0068 0.1592 3.0068
nonbonded NH2 0.1592 3.0068 0.1592 3.0068
nonbonded NH3 0.1592 3.0068 0.1592 3.0068
nonbonded O 0.2342 2.7755 0.2342 3.0068 ! 1.688 1.519 1.350 1.266
nonbonded OC 1.0244 2.7755 1.0244 3.0068
nonbonded OH 0.2342 2.7755 0.2342 3.0068
nonbonded S 0.0239 3.7458 0.0239 3.5300 ! 2.102 1.892 1.682 1.577
! 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
set message on echo on end
Contact the webmaster for help, if required. Friday, April 19, 2024 3:23:12 AM GMT (wattos1)