Dear modellers, I'd like to use the "make_restraint" command in my top file, in order to obtain five models that have a b-sheet in a particular region, but it doesn't work, in the final five models (after doing 100 cicles of VTFM) the b-sheet disappears (and the two strands too), while it is present in the .ini file, please, can you tell me something about this problem? the top file I used is the following:
INCLUDE
SET ALNFILE = 'align.ali' SET KNOWNS = 'E1' 'M1' ' SET SEQUENCE = 'abs' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'STRAND', RESIDUE_IDS = '148:' '150:'
MAKE_RESTRAINTS RESTRAINT_TYPE = 'STRAND', RESIDUE_IDS = '158:' '160:'
#antiparallel sheet MAKE_RESTRAINTS RESTRAINT_TYPE = 'SHEET', ATOM_IDS = 'N:148' 'O:160', SHEET_H-BONDS = -5 RETURN END_SUBROUTINE
-- dott. Paola D'Alessio Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio@unisa.it