[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

about restraints

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: