Simulated annealing


Here a structure is calculated using experimentally measured interproton distance estimates, hydrogen bonds and coupling-constant-derived dihedral angle restraints. This protocol uses ab initio simulated annealing starting from an extended template structure (see previous sections). The structure calculation is performed with the CNS task file anneal.inp.

      cns_solve < anneal.inp > anneal.out [45 minutes]

In this case five trial structures were generated. An alternative approach would have been to only generated accepted structures, in which case the script would have run until five accepted structures had been generated. The five structures are quite similar:

Five structures calculated from simulated annealing.

A summary of the structure calculation is written at the top of each output PDB file:

REMARK The macromolecule has 118 residues
REMARK Trial structure 1 of 5 structures
REMARK Molecular dynamics scheme : torsion; torsion; cartesian; minimize
REMARK High temperature dynamics :
REMARK      temp: 50000 steps: 1000 time(ps): 15
REMARK 1st cooling stage         :
REMARK      temp: 50000->0 steps: 1000 time(ps): 15 temp step: 250
REMARK 2nd cooling stage          :
REMARK      temp: 2000->0 steps: 3000 time(ps): 15 temp step: 25
REMARK a total 2000 steps of minimization
REMARK VDW scale factors 0.1; 0.1->1; 1->4; 1
REMARK 2617 NOEs in 2 class(es) with scale factors of 150; 150; 150; 75
REMARK      averaging function(s): sum, hbnd: sum
REMARK 0 3-bond j-couplings in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 1-bond j-couplings in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 carbon chemical shifts in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 proton chemical shifts in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 diffusion anisotropy restraints in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 susceptability anisotropy restraints in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 325 dihedral restraints with scale factors of 100; 200; 200; 400
REMARK 0 planarity restraints with a scale factor of NA
REMARK NCS restraints not used.
REMARK ===============================================================
REMARK               bond, angles, improp, vdw(<1.6),  dihed
REMARK violations :     2       8       5         4      49
REMARK RMSD       : 0.0041   0.634   0.577            25.016
REMARK ===============================================================
REMARK                noe,   cdih,   coup,   oneb, carb-a, carb-b,
REMARK violations :     0       1       0       0       0   -----
REMARK RMSD       :  0.022   0.729   0.000   0.000   0.000   0.000
REMARK 0.2/2 viol.:     7       6       0
REMARK ===============================================================
REMARK               dani,   sani
REMARK violations :     0       0
REMARK RMSD       :  0.000   0.000
REMARK .2/.1 viol.:     0       0
REMARK ===============================================================
REMARK Protons       violations, rmsd
REMARK all    :           0       0.000
REMARK class 1:           0       0.000
REMARK class 2:           0       0.000
REMARK class 3:           0       0.000
REMARK class 4:           0       0.000
REMARK ===============================================================
REMARK overall = 529.078
REMARK bon     = 31.2461
REMARK ang     = 204.65
REMARK imp     = 47.5888
REMARK vdw     = 133.24
REMARK harm    = 0
REMARK noe     = 91.3054
REMARK coup    = 0
REMARK oneb    = 0
REMARK carb    = 0
REMARK prot    = 0
REMARK dani    = 0
REMARK sani    = 0
REMARK cdih    = 21.0478
REMARK ncs     = 0
REMARK ===============================================================
REMARK DATE: 8-Jul-99  18:18:29       created by user: paul
REMARK VERSION:0.5
ATOM      1  CA  MET     1      -9.804  10.394  -1.108  1.00  0.00      A
ATOM      2  HA  MET     1      -9.550  11.372  -0.727  1.00  0.00      A

The information about violations can be used manually to select acceptable structures. Instead the CNS task file accept.inp can be used to identify acceptable structures and to calculate an average conformation:

      cns_solve < accept.inp > accept.out [2.5 minutes]

Information about accepted structures, violations and variations between structures is printed at the top of the average structure:

REMARK The macromolecule has 118 residues
REMARK Accepted structures 5 of 5 structures
REMARK 2617 NOEs in 2 class(es)
REMARK      averaging function(s): sum, hbnd: sum
REMARK 0 3-bond j-couplings in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 1-bond j-couplings in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 carbon chemical shifts in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 proton chemical shifts in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 diffusion anisotropy restraints in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 0 susceptability anisotropy restraints in 0 class(es) with
REMARK      scale factor(s) of NA
REMARK 325 dihedral restraints
REMARK 0 planarity restraints with a scale factor of NA
REMARK NCS restraints not used.
REMARK ===============================================================
REMARK          viol   +/-  sd       rmsd   +/- sd
REMARK Bond   :   2.00 +/-   0.000   0.0039 +/- 0.00017
REMARK Angl   :   8.20 +/-   0.447   0.6118 +/- 0.0136
REMARK Impr   :   2.60 +/-   1.342   0.4901 +/- 0.0494
REMARK VDW    :   1.80 +/-   1.304
REMARK Dihed  :  47.00 +/-   2.915   24.653 +/- 0.4696
REMARK ===============================================================
REMARK          viol   +/-  sd       rmsd   +/-  sd
REMARK NOE    :   0.00 +/-   0.000   0.0200 +/-  0.0009
REMARK cdih   :   1.00 +/-   0.000   0.6005 +/-  0.0711
REMARK J-coup :   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK Oneb   :   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK ===============================================================
REMARK         viol   +/-  sd     rmsd A +/-  sd     rmsd B +/- sd
REMARK Carb  :   0.00 +/-  0.000   0.000 +/-  0.000   0.000 +/-  0.000
REMARK ===============================================================
REMARK Protons  viol   +/-  sd       rmsd   +/-  sd
REMARK all    :   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK class 1:   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK class 2:   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK class 3:   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK class 4:   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK ===============================================================
REMARK          viol   +/-  sd       rmsd   +/-  sd
REMARK dani   :   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK sani   :   0.00 +/-   0.000   0.0000 +/-  0.0000
REMARK ===============================================================
REMARK overall =   441.00 +/-    44.01
REMARK bond    =    27.36 +/-     2.41
REMARK angle   =   190.47 +/-     8.58
REMARK improp  =    34.63 +/-     7.37
REMARK vdw     =   102.84 +/-    17.14
REMARK harm    =     0.00 +/-     0.00
REMARK noe     =    78.47 +/-     7.58
REMARK coup    =     0.00 +/-     0.00
REMARK oneb    =     0.00 +/-     0.00
REMARK carb    =     0.00 +/-     0.00
REMARK prot    =     0.00 +/-     0.00
REMARK dani    =     0.00 +/-     0.00
REMARK sani    =     0.00 +/-     0.00
REMARK cdih    =     7.22 +/-     1.82
REMARK ncs     =     0.00 +/-     0.00
REMARK ===============================================================
REMARK rms around the mean for selection   =  0.603 +/- 0.4288
REMARK rms around the mean for non-h atoms =  0.850 +/- 0.5029
REMARK ===============================================================
REMARK pairwise rms
REMARK atom selection:  0.920 +/- 0.2895  min:  0.550  max:  1.305
REMARK non-hydrogen  :  1.203 +/- 0.1997  min:  0.924  max:  1.483
REMARK ===============================================================
REMARK DATE:13-Jul-99  12:33:27       created by user: paul
REMARK VERSION:0.5
ATOM      1  CA  MET     1      -9.639  10.257  -0.958  1.00  0.70      A
ATOM      2  HA  MET     1      -9.301  11.261  -0.749  1.00  0.73      A

Script to run this tutorial

Back to tutorials   Next section