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 --------------------------------------------
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 > --------------------------------------------
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Dong Xu -
Prevost Martine