Re: "STARTING_MODEL" and"ENDING_MODEL"

23 May 2000


      Dear Dr. Zhang,
I believe it is not necessarily a good idea to use modeller for a heptapeptide
modeling based on another heptapeptide unless you are sure that they adopt a
very similar conformation.  I do not know what is your environment (is it a
docked peptide on a protein surface, or is it in solvent etc.) but there is no
guarantee that even the same heptapeptide will have the same conformation in
different environments.
Modeller relies on utilising the idea of evolution, that full size,
sequentially   similar proteins in physiological environment (for which
modeller basically does not account for) adopt similar folds, while small
peptides rely more on energetic criteria, which is not what modeller was
designed for.
Nevertheless:
> I also noticed that the backbone conformation of the model and the template is
> different. This is what I would like to overcome if possible. Probably I missed
> something in my top file if modeller can do this kind of work. Here is my top
> file.
Modeller builds a model based on the given restraints derived from statistical
observations of features from other proteins,  from molecular mechanics
forcefields and your template. These retrains  will not necessarily  guide the
model to entirely the same conformation as the  template. As i checked your
model and template I would say that is pretty much what one would expect.
As I mentioned above, in case of such a short fragment one is fairly lost,
having no solid reference, and  maybe way off reality.
If you want to force  modeling to deal only with sidechains and retain the same
backbone conformation include in your top file:
SUBROUTINE ROUTINE = 'select_atoms'
  PICK_ATOMS SELECTION_SEGMENT='@:@' 'X:X',;
   SELECTION_SEARCH='segment', PICK_ATOMS_SET=1, ;
   RES_TYPES='all', ATOM_TYPES='SDCH', ;
   SELECTION_FROM='all', SELECTION_STATUS='initialize'
  RETURN
END_SUBROUTINE
but I mention again that to my opinion it is an inadequate use of Modeller. I
would prefer some detailed mol mechanics or semi empirical  forcefields as
CHARMM, AMBER or ECEPP, preferably with solvent representation and exhaustive
optimisation method.
Sincerely,
Andras Fiser
> > # Homology modelling > > INCLUDE > TOP routines > SET OUTPUT_CONTROL= 1 1 1 1 > SET ALNFILE  = 'peptide_1.ali' > SET KNOWNS   = '1dkxB' > SET SEQUENCE = 'peptide_1' > SET ATOM_FILES_DIRECTORY > fileSET STARTING_MODEL= 1 > SET ENDING_MODEL  = 1 > > how many models to calculate) > > CALL ROUTINE = 'model' > > SET FINAL_MALIGN3D = 1 > > And I also attached > > Thank you for your time. > > Sincerely, > > Xiao-Ping Zhang > > Andras Fiser wrote: > > > Hi > > > > STARTING and > > the structure > > differences > > the structure > > insertions, > > the template etc.). > > > > These variables > > by Azat: technically > > circumstances, > > generate 10 > > ENDING_MODEL=20) etc. > > > > > I am modeling > > > STARTING_MODEL=1, > > > orientations > > > can overlap > > > coordinates), > > > the same > > > > if you include > > SET FINAL_MALIGN3D = 1 > > > > modeller will > > generate the > > > > or you can write > > any sources > > commands. > > > > Andras > > > > -- > >     , > > Andras Fiser, PhD > > The Rockefeller University > > Box 270, 1230 York Avenue > > New York, NY > > ****************************** > Xiao-Ping Zhang > Department of Biochemistry > Arrhenius Laboratories > Stockholm Universities > 106 91 Stockholm > Sweden > > Phone:  046-08-162472 /162582 > Fax:    046-08-153679 > e-mail: zhang@biokemi.su.se > >   ------------------------ > ATOM   1666  N   ASN B   1 > ATOM   1667  CA  ASN B   1 > ATOM   1668  C   ASN B   1 > ATOM   1669  O   ASN B   1 > ATOM   1670  CB  ASN B   1 > ATOM   1671  CG  ASN B   1 > ATOM   1672  OD1 ASN B   1 > ATOM   1673  ND2 ASN B   1 > ATOM   1674  N   ARG B   2 > ATOM   1675  CA  ARG B   2 > ATOM   1676  C   ARG B   2 > ATOM   1677  O   ARG B   2 > ATOM   1678  CB  ARG B   2 > ATOM   1679  CG  ARG B   2 > ATOM   1680  CD  ARG B   2 > ATOM   1681  NE  ARG B   2 > ATOM   1682  CZ  ARG B   2 > ATOM   1683  NH1 ARG B   2 > ATOM   1684  NH2 ARG B   2 > ATOM   1685  N   LEU B   3 > ATOM   1686  CA  LEU B   3 > ATOM   1687  C   LEU B   3 > ATOM   1688  O   LEU B   3 > ATOM   1689  CB  LEU B   3 > ATOM   1690  CG  LEU B   3 > ATOM   1691  CD1 LEU B   3 > ATOM   1692  CD2 LEU B   3 > ATOM   1693  N   LEU B   4 > ATOM   1694  CA  LEU B   4 > ATOM   1695  C   LEU B   4 > ATOM   1696  O   LEU B   4 > ATOM   1697  CB  LEU B   4 > ATOM   1698  CG  LEU B   4 > ATOM   1699  CD1 LEU B   4 > ATOM   1700  CD2 LEU B   4 > ATOM   1701  N   LEU B   5 > ATOM   1702  CA  LEU B   5 > ATOM   1703  C   LEU B   5 > ATOM   1704  O   LEU B   5 > ATOM   1705  CB  LEU B   5 > ATOM   1706  CG  LEU B   5 > ATOM   1707  CD1 LEU B   5 > ATOM   1708  CD2 LEU B   5 > ATOM   1709  N   THR B   6 > ATOM   1710  CA  THR B   6 > ATOM   1711  C   THR B   6 > ATOM   1712  O   THR B   6 > ATOM   1713  CB  THR B   6 > ATOM   1714  OG1 THR B   6 > ATOM   1715  CG2 THR B   6 > ATOM   1716  N   GLY B   7 > ATOM   1717  CA  GLY B   7 > ATOM   1718  C   GLY B   7 > ATOM   1719  O   GLY B   7 > ATOM   1720  OXT GLY B   7 > >   ------------------------ > REMARK Produced by MODELLER:  unknown > ATOM   1666  N   ASN B   1 > ATOM   1667  CA  ASN B   1 > ATOM   1668  C   ASN B   1 > ATOM   1669  O   ASN B   1 > ATOM   1670  CB  ASN B   1 > ATOM   1671  CG  ASN B   1 > ATOM   1672  OD1 ASN B   1 > ATOM   1673  ND2 ASN B   1 > ATOM   1674  N   ARG B   2 > ATOM   1675  CA  ARG B   2 > ATOM   1676  C   ARG B   2 > ATOM   1677  O   ARG B   2 > ATOM   1678  CB  ARG B   2 > ATOM   1679  CG  ARG B   2 > ATOM   1680  CD  ARG B   2 > ATOM   1681  NE  ARG B   2 > ATOM   1682  CZ  ARG B   2 > ATOM   1683  NH1 ARG B   2 > ATOM   1684  NH2 ARG B   2 > ATOM   1685  N   LEU B   3 > ATOM   1686  CA  LEU B   3 > ATOM   1687  C   LEU B   3 > ATOM   1688  O   LEU B   3 > ATOM   1689  CB  LEU B   3 > ATOM   1690  CG  LEU B   3 > ATOM   1691  CD1 LEU B   3 > ATOM   1692  CD2 LEU B   3 > ATOM   1693  N   LEU B   4 > ATOM   1694  CA  LEU B   4 > ATOM   1695  C   LEU B   4 > ATOM   1696  O   LEU B   4 > ATOM   1697  CB  LEU B   4 > ATOM   1698  CG  LEU B   4 > ATOM   1699  CD1 LEU B   4 > ATOM   1700  CD2 LEU B   4 > ATOM   1701  N   LEU B   5 > ATOM   1702  CA  LEU B   5 > ATOM   1703  C   LEU B   5 > ATOM   1704  O   LEU B   5 > ATOM   1705  CB  LEU B   5 > ATOM   1706  CG  LEU B   5 > ATOM   1707  CD1 LEU B   5 > ATOM   1708  CD2 LEU B   5 > ATOM   1709  N   THR B   6 > ATOM   1710  CA  THR B   6 > ATOM   1711  C   THR B   6 > ATOM   1712  O   THR B   6 > ATOM   1713  CB  THR B   6 > ATOM   1714  OG1 THR B   6 > ATOM   1715  CG2 THR B   6 > ATOM   1716  N   GLY B   7 > ATOM   1717  CA  GLY B   7 > ATOM   1718  C   GLY B   7 > ATOM   1719  O   GLY B   7 > ATOM   1720  OXT GLY B   7 > >   ------------------------ > REMARK Produced by MODELLER:  unknown > REMARK Produced by MODELLER:  unknown > REMARK MODELLER OBJECTIVE FUNCTION: > ATOM      1  N   LEU     1 > ATOM      2  CA  LEU     1 > ATOM      3  CB  LEU     1 > ATOM      4  CG  LEU     1 > ATOM      5  CD2 LEU     1 > ATOM      6  CD1 LEU     1 > ATOM      7  C   LEU     1 > ATOM      8  O   LEU     1 > ATOM      9  N   ARG     2 > ATOM     10  CA  ARG     2 > ATOM     11  CB  ARG     2 > ATOM     12  CG  ARG     2 > ATOM     13  CD  ARG     2 > ATOM     14  NE  ARG     2 > ATOM     15  CZ  ARG     2 > ATOM     16  NH1 ARG     2 > ATOM     17  NH2 ARG     2 > ATOM     18  C   ARG     2 > ATOM     19  O   ARG     2 > ATOM     20  N   ARG     3 > ATOM     21  CA  ARG     3 > ATOM     22  CB  ARG     3 > ATOM     23  CG  ARG     3 > ATOM     24  CD  ARG     3 > ATOM     25  NE  ARG     3 > ATOM     26  CZ  ARG     3 > ATOM     27  NH1 ARG     3 > ATOM     28  NH2 ARG     3 > ATOM     29  C   ARG     3 > ATOM     30  O   ARG     3 > ATOM     31  N   ALA     4 > ATOM     32  CA  ALA     4 > ATOM     33  CB  ALA     4 > ATOM     34  C   ALA     4 > ATOM     35  O   ALA     4 > ATOM     36  N   SER     5 > ATOM     37  CA  SER     5 > ATOM     38  CB  SER     5 > ATOM     39  OG  SER     5 > ATOM     40  C   SER     5 > ATOM     41  O   SER     5 > ATOM     42  N   LEU     6 > ATOM     43  CA  LEU     6 > ATOM     44  CB  LEU     6 > ATOM     45  CG  LEU     6 > ATOM     46  CD2 LEU     6 > ATOM     47  CD1 LEU     6 > ATOM     48  C   LEU     6 > ATOM     49  O   LEU     6 > ATOM     50  N   GLY     7 > ATOM     51  CA  GLY     7 > ATOM     52  C   GLY     7 > ATOM     53  O   GLY     7 > ATOM     54  OXT GLY     7 > END

by the MODELLER TOP routine 'model'. # Include the predefined # alignment filename # codes of the templates # code of the target = './:../atom_files'   # directories for input atom # index of the first model # index of the last model # (determines # do homology modelling the model and template. ENDING model variables define how many models to generate. Because optimization is stochastic  (MD simulation) you can expect minor among different structures, especially if you have such regions in which are not very well defined by restraints (segments with vicinity of deletions or  loosely defined substrates  relative to also define the extension of your model files as it was noted it is useful if you run modeling under  different e.g. generate 10 models with one ligand between 1-10, than models using different ligand or templates (Starting MODEL=11, a very short peptide with modeller4. If I set ENDING_MODEL=10, I get 10 models which have different and spatial location. If I would like to get a model which with the original model (maximum uses the template how to do it? And is it possible to keep the backbone  in conformation of original peptide ? in your top file: automatically superpose all your models onto the template and *fit files which contains strcutures whith supeprosed coordinates. a short top script to superpose any number of structures from generated, as explained in the manual under MALIGN3D and  SUPERPOSE # phone: (212) 327 7206 # fax:   (212) 327 7540 # e-mail:fisera@rockefeller.edu 10021-6399, USA # http://salilab.org/~andras of Natural Sciences ------------------------------------------------------- 50.702  87.722  38.867  1.00 43.10           N 51.449  86.814  37.946  1.00 41.67           C 51.328  87.331  36.498  1.00 39.68           C 50.267  87.216  35.865  1.00 39.73           O 50.874  85.389  38.031  1.00 44.13           C 50.750  84.878  39.468  1.00 46.27           C 50.338  85.626  40.353  1.00 46.16           O 51.084  83.634  39.757  1.00 45.47           N 52.433  87.895  36.025  1.00 36.65           N 52.555  88.448  34.656  1.00 32.06           C 53.586  87.620  33.873  1.00 28.54           C 54.665  87.294  34.387  1.00 25.94           O 53.006  89.911  34.728  1.00 36.71           C 52.282  90.816  33.727  1.00 41.73           C 50.777  90.927  33.989  1.00 44.15           C 50.050  91.548  32.870  1.00 47.60           N 48.751  91.877  32.904  1.00 47.23           C 48.009  91.654  33.997  1.00 49.83           N 48.094  92.442  31.880  1.00 44.33           N 53.236  87.297  32.635  1.00 25.64           N 54.079  86.438  31.778  1.00 22.32           C 54.737  87.207  30.621  1.00 22.74           C 54.225  88.243  30.169  1.00 22.20           O 53.235  85.323  31.158  1.00 18.68           C 52.213  84.739  32.134  1.00 19.46           C 51.449  83.546  31.556  1.00 20.46           C 52.846  84.236  33.433  1.00 15.12           C 55.858  86.627  30.205  1.00 20.92           N 56.688  87.110  29.086  1.00 23.64           C 56.790  86.014  28.021  1.00 27.49           C 56.680  84.818  28.324  1.00 28.91           O 58.117  87.414  29.559  1.00 25.41           C 58.192  88.438  30.690  1.00 24.73           C 59.616  88.631  31.223  1.00 24.26           C 57.716  89.830  30.272  1.00 24.71           C 57.000  86.447  26.792  1.00 29.48           N 57.145  85.533  25.643  1.00 30.37           C 58.628  85.360  25.284  1.00 31.29           C 59.481  86.132  25.727  1.00 27.62           O 56.468  86.114  24.395  1.00 32.09           C 55.053  86.640  24.629  1.00 35.07           C 54.403  87.181  23.350  1.00 40.10           C 54.100  85.569  25.156  1.00 38.35           C 58.897  84.333  24.478  1.00 36.46           N 60.264  84.053  23.927  1.00 44.50           C 60.360  84.677  22.466  1.00 47.61           C 59.699  84.184  21.554  1.00 48.64           O 60.477  82.528  23.817  1.00 47.63           C 59.676  81.818  24.755  1.00 53.22           O 61.928  82.107  24.047  1.00 48.63           C 61.232  85.767  22.212  1.00 50.38           N 61.334  86.583  20.844  1.00 51.64           C 62.588  86.267  20.033  1.00 53.33           C 63.180  85.187  20.170  1.00 53.27           O 62.917  87.254  19.203  1.00 53.00           O ------------------------------------------------------- unknown                                1 50.702  87.722  38.867  1.00 43.10           N 51.449  86.814  37.946  1.00 41.67           C 51.328  87.331  36.498  1.00 39.68           C 50.267  87.216  35.865  1.00 39.73           O 50.874  85.389  38.031  1.00 44.13           C 50.750  84.878  39.468  1.00 46.27           C 50.338  85.626  40.353  1.00 46.16           O 51.084  83.634  39.757  1.00 45.47           N 52.433  87.895  36.025  1.00 36.65           N 52.555  88.448  34.656  1.00 32.06           C 53.586  87.620  33.873  1.00 28.54           C 54.665  87.294  34.387  1.00 25.94           O 53.006  89.911  34.728  1.00 36.71           C 52.282  90.816  33.727  1.00 41.73           C 50.777  90.927  33.989  1.00 44.15           C 50.050  91.548  32.870  1.00 47.60           N 48.751  91.877  32.904  1.00 47.23           C 48.009  91.654  33.997  1.00 49.83           N 48.094  92.442  31.880  1.00 44.33           N 53.236  87.297  32.635  1.00 25.64           N 54.079  86.438  31.778  1.00 22.32           C 54.737  87.207  30.621  1.00 22.74           C 54.225  88.243  30.169  1.00 22.20           O 53.235  85.323  31.158  1.00 18.68           C 52.213  84.739  32.134  1.00 19.46           C 51.449  83.546  31.556  1.00 20.46           C 52.846  84.236  33.433  1.00 15.12           C 55.858  86.627  30.205  1.00 20.92           N 56.688  87.110  29.086  1.00 23.64           C 56.790  86.014  28.021  1.00 27.49           C 56.680  84.818  28.324  1.00 28.91           O 58.117  87.414  29.559  1.00 25.41           C 58.192  88.438  30.690  1.00 24.73           C 59.616  88.631  31.223  1.00 24.26           C 57.716  89.830  30.272  1.00 24.71           C 57.000  86.447  26.792  1.00 29.48           N 57.145  85.533  25.643  1.00 30.37           C 58.628  85.360  25.284  1.00 31.29           C 59.481  86.132  25.727  1.00 27.62           O 56.468  86.114  24.395  1.00 32.09           C 55.053  86.640  24.629  1.00 35.07           C 54.403  87.181  23.350  1.00 40.10           C 54.100  85.569  25.156  1.00 38.35           C 58.897  84.333  24.478  1.00 36.46           N 60.264  84.053  23.927  1.00 44.50           C 60.360  84.677  22.466  1.00 47.61           C 59.699  84.184  21.554  1.00 48.64           O 60.477  82.528  23.817  1.00 47.63           C 59.676  81.818  24.755  1.00 53.22           O 61.928  82.107  24.047  1.00 48.63           C 61.232  85.767  22.212  1.00 50.38           N 61.334  86.583  20.844  1.00 51.64           C 62.588  86.267  20.033  1.00 53.33           C 63.180  85.187  20.170  1.00 53.27           O 62.917  87.254  19.203  1.00 53.00           O ------------------------------------------------------- unknown                                1 unknown                                1 26.9688 55.010  84.333  35.414  1.00   .65       1SG   2 53.968  85.226  35.960  1.00   .65       1SG   3 54.576  86.546  36.460  1.00   .65       1SG   4 55.517  86.395  37.669  1.00   .65       1SG   5 55.807  87.761  38.311  1.00   .65       1SG   6 56.797  85.616  37.318  1.00   .65       1SG   7 52.984  85.564  34.899  1.00   .65       1SG   8 52.463  84.686  34.216  1.00   .65       1SG   9 52.699  86.870  34.759  1.00   .93       1SG  10 51.769  87.286  33.762  1.00   .93       1SG  11 51.341  88.752  33.924  1.00   .93       1SG  12 49.987  89.081  33.293  1.00   .93       1SG  13 48.810  88.536  34.111  1.00   .93       1SG  14 48.986  89.024  35.510  1.00   .93       1SG  15 48.532  90.257  35.886  1.00   .93       1SG  16 47.868  91.051  34.997  1.00   .93       1SG  17 48.729  90.696  37.163  1.00   .93       1SG  18 52.490  87.139  32.464  1.00   .93       1SG  19 53.008  86.065  32.159  1.00   .93       1SG  20 52.564  88.223  31.668  1.00   .88       1SG  21 53.229  88.095  30.409  1.00   .88       1SG  22 52.989  89.248  29.411  1.00   .88       1SG  23 53.492  90.618  29.887  1.00   .88       1SG  24 53.730  91.607  28.738  1.00   .88       1SG  25 52.428  92.217  28.346  1.00   .88       1SG  26 52.025  93.407  28.885  1.00   .88       1SG  27 52.803  94.045  29.807  1.00   .88       1SG  28 50.851  93.977  28.488  1.00   .88       1SG  29 54.698  88.058  30.662  1.00   .88       1SG  30 55.161  88.076  31.802  1.00   .88       1SG  31 55.461  87.968  29.562  1.00   .49       1SG  32 56.886  87.958  29.616  1.00   .49       1SG  33 57.464  86.858  30.523  1.00   .49       1SG  34 57.312  87.656  28.224  1.00   .49       1SG  35 56.570  87.027  27.470  1.00   .49       1SG  36 58.516  88.102  27.828  1.00   .41       1SG  37 58.909  87.798  26.491  1.00   .41       1SG  38 59.982  88.738  25.914  1.00   .41       1SG  39 59.411  90.008  25.645  1.00   .41       1SG  40 59.458  86.415  26.493  1.00   .41       1SG  41 60.492  86.133  27.098  1.00   .41       1SG  42 58.736  85.510  25.810  1.00   .40       1SG  43 59.134  84.144  25.669  1.00   .40       1SG  44 57.933  83.183  25.626  1.00   .40       1SG  45 57.147  83.103  26.955  1.00   .40       1SG  46 58.071  82.759  28.139  1.00   .40       1SG  47 55.963  82.127  26.846  1.00   .40       1SG  48 59.804  84.111  24.339  1.00   .40       1SG  49 60.999  83.838  24.235  1.00   .40       1SG  50 59.034  84.403  23.277  1.00   .24       1SG  51 59.619  84.472  21.974  1.00   .24       1SG  52 59.258  83.201  21.229  1.00   .24       1SG  53 58.244  82.561  21.606  1.00   .24       1SG  54 59.994  82.858  20.266  1.00   .24       1SG  55
-- 
    ,
Andras Fiser, PhD            # phone: (212) 327 7206
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:fisera@rockefeller.edu
New York, NY 10021-6399, USA # http://salilab.org/~andras