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: mprevost@ulb.ac.be > --------------------------------------------