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Re:



Hi Martine,

I have done some modeling using NMR restraints. The following files show an
example that I modeled successfully using MODELLER.

The following is the *.top file:

# Homology modelling by the MODELLER TOP routine model

INCLUDE                                # Include predefined TOP routines

SET TOPLIB = '${LIB}/top_allh.lib'     # topology library
SET TOPOLOGY_MODEL = 1                 # corresponding topology model;
SET PARLIB = '${LIB}/par.lib'          # parameters library

SET HYDROGEN_IO = 'ON'                 # include hydrogen atoms
SET HETATM_IO = 'ON'                   # include HETATM entries

SET ALNFILE  = '2ptl.ali'              # alignment filename
SET KNOWNS   = '2ptl'                  # template name
SET SEQUENCE = '2igh'                  # target sequence

CALL ROUTINE = 'model'                 # do homology modelling

# Redefine the rd_restraints routine:
SUBROUTINE ROUTINE = 'rd_restraints'
READ_RESTRAINTS FILE = CSRFILE

# This is an additional user provided file:

READ_RESTRAINTS FILE = 'nmr_2igh.rsr'
RETURN
END_SUBROUTINE

---------------------------------------------------

Prepare the "nmr_2igh.rsr" file in the following format:

MODELLER12 VERSION: USER FORMAT
R   3  1  1 28  2  2  0    2.9000    0.2000     HN:52      HB#:52
R   3  1  1 28  2  2  0    3.4000    0.2000     HN:49      HA:59
R   3  1  1 28  2  2  0    2.9000    0.2000     HN:48      HB#:48
R   3  1  1 28  2  2  0    2.9000    0.2000     HN:31      HB:30
R   3  1  1 28  2  2  0    4.0000    0.2000     HN:59      HG##:59
R   3  1  1 28  2  2  0    3.4000    0.2000     HN:25      HB#:24
R   3  1  1 28  2  2  0    3.4000    0.2000     HN:60      HG##:59
......

Hope it helps.

-Dong
http://compbio.ornl.gov/~nxy


Prevost Martine wrote:

> Hello,
>
> I would like to introduce a restrained distance between two atoms when
> generating a model with Modeller. Unfortunately when the two atoms for
> which I would like to retrain the distance are specified in my top file,
> the program seems to interpret this as all atoms between these two are
> concerned by possible restraints ?? I believe that when one wants to
> introduce restraints from NMR data that's what one wishes to do, i.e.
> specify pairs of atoms (one or many more) for which the distance should be
> within a certain range. Could somebody explain to me how the Modeller
> input should be modified so as to introduce such restraints ? Thank you
> very much.
>
> Martine.
>
>
>  --------------------------------------------
>   Martine Prevost
>   Ingenierie Biomoleculaire, CP 165/64
>   Universite Libre de Bruxelles
>   50 avenue Franklin Roosevelt
>   B-1050 Bruxelles
>   Belgium
>   Phone : 32-2-650 2049
>   Fax   : 32-2-650 3606
>   E-mail: 
> --------------------------------------------