dear sir , I am trying to model a protein using an alignment to a pdb template and nmr data for a loop which is missing in the pdb template. the input top file that used is the following:
INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file
SET ATOM_FILES_DIRECTORY = './' SET PDB_EXT = '.pdb' #SET MD_LEVEL = 'refine1' SET HYDROGEN_IO = on #SET DEVIATION = 4.0 SET ALIGNMENT_FORMAT = 'PIR' SET STARTING_MODEL = 1 SET ENDING_MODEL = 10 SET SEQUENCE = 'mysequence' SET ALNFILE = 'my.ali' SET KNOWNS='mytemplatestructure'
SET TOPOLOGY_MODEL = 1 SET TOPLIB = '/software/modeller7v7/modlib/top_allh.lib' SET PARLIB = '/software/modeller7v7/modlib/par.lib' CALL ROUTINE = 'model'
SUBROUTINE ROUTINE = 'rd_restraints' READ_RESTRAINTS FILE = CSRFILE # This is an additional user provided file: READ_RESTRAINTS FILE = 'nmr.rsr' RETURN END_SUBROUTINE
I obtained 10 models but I can see that none of them satisfies all the nmr restraints. therefore I thought to model more thoroughly only the loop for which I have the
nmr restraints.
could you suggest me how to include in the proper way when I call the loop routine? shall I use again
SUBROUTINE ROUTINE = 'rd_restraints' READ_RESTRAINTS FILE = CSRFILE # This is an additional user provided file: READ_RESTRAINTS FILE = 'nmr.rsr' RETURN END_SUBROUTINE ? or shoud I read only the nmr.rsr? or other options?
-many thanks mvcubellis
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