Hello, my name is Matthias and I'm a PhD Student at University of Saarland. I'm trying to model a cypP450 with modeller7v7 by defining the secondary structure (alpha, sheet..) in the special_restraints ROUTINE, but I still get error messages and the job is broken up!
That's the error message I got: "Dynamically allocated memory at amaxseq [B,kB,MB]: 39334681 38412.773 37.512 TOP_________> 169 174 CALL ROUTINE = 'special_restraints'
TOP_________> 170 479 SET ADD_RESTRAINTS = ON
TOP_________> 171 480 MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '; 228:A' '253:A'
assgn___215E> Dynamic memory allocation failed. Routine, variable, status: vars%val 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1"
While my top file (special_restraints) is: "SUBROUTINE ROUTINE = 'special_restraints'
SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '228:A' '253:A' MAKE_RESTRAINTS RESTRAINT_TYPE = 'ALPHA', RESIDUE_IDS = '140:A' '159:A' MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '464:A' '467:A' MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '480:A' '484:A' MAKE_RESTRAINTS RESTRAINT_TYPE= 'SHEET', RESIDUE_IDS = '490:A' '495:A'
RETURN END_SUBROUTINE"
1.Can you tell me what the reason for failing is? 2.Further, does modeller8.1 resolve this problem (if there is a bug in mod7v7?)! 3.I even get the error disclaimer: "openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 196 233 WRITE_SCHEDULE FILE = SCHFILE
openf5__224_> Open 14 UNKNOWN SEQUENTIAL CYP17.sch TOP_________> 197 234 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1
TOP_________> 198 235 CALL ROUTINE = 'single_model_pass'
TOP_________> 199 253 READ_MODEL FILE = MODEL,MODEL_SEGMENT = '31:A' '496:A'
openf5__224_> Open 11 OLD SEQUENTIAL Mixed1.ini openf5__224_> Open 11 OLD SEQUENTIAL Mixed1.ini rdatm___297_> Segments, residues, atoms: 1 466 7457 rdatm___298_> Segment: 1 31 A 496 A 7457 TOP_________> 200 254 DO SCHEDULE_STEP = 1 N_SCHEDULE 1
TOP_________> 201 255 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1
TOP_________> 202 256 PICK_RESTRAINTS ADD_RESTRAINTS = OFF
nselat__596E> Atom index is out of range (iatm,natm): 7458 7457 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 39111561 " What's the reason for, where I do mistakes?
Thanks in advance,
Matthias Negri
8.2 Pharmaceutical and Medicinal Chemistry Saarland University P.O.Box 151150 66041 Saarbrücken, Germany phone: +49-681-302-2980 fax: +49-681-302-4386 Email: m.negri@mx.uni-saarland.de http://www.uni-saarland.de/fak8/hartmann
Computational Medicinal Chemistry Group Dept. of Pharmaceutical Sciences, University of Bologna Via Belmeloro, 6; 40100 Bologna, Italy Email: thias@scfarm.unibo.it http://www.scfarm.unibo.it