How do I (or is it possible to ) to specify the solvent accessibility of residues with ACCESSIBILITY_TYPE in MAKE_CONSTRAINTS ? Is there a specific RESTRAINT_TYPE associated with it ?
Here is my input
# Test for restraints on accessibility (?) READ_TOPOLOGY FILE '$(LIB)/top_heav.lib' READ_PARAMETERS FILE ='$(LIB)/par.lib' SET ATOM_FILES_DIRECTORY = './' READ_MODEL FILE = 'test.ent', MODEL_SEGMENT = '1:' '7:' SEQUENCE_TO_ALI ATOM_FILES = 'test.ent', ALIGN_CODES = 'test.ali' SEQUENCE_TO_ALI ADD_SEQUENCE = on , ATOM_FILES = ATOM_FILES 'test.ini', ; ALIGN_CODES = ALIGN_CODES 'test-ini' GENERATE_TOPOLOGY SEQUENCE = 'test-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE 'test.ini' SET ACCESSIBILITY_TYPE = 8 MAKE_RESTRAINTS RESTRAINT_TYPE = 'sphere' WRITE_RESTRAINTS FILE = 'test-1.rsr' ENERGY DYNAMIC_SPHERE = off ENERGY WRITE_DATA FILE = 'test' , OUTPUT='psa'
Thanks Germana Paterlini
Department of Medicinal Chemistry University of Minnesota Minneapolis, MN 55455