Hi Modellers
I wonder if anyone can help me solve a problem I'm having with modeller. I'm using two templates to construct a model of a protein. Modeller stops with the following messages
iup2crm_E> IUPAC atom not found in topology library: OG iup2crm_E> residue type undefined recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1
This happens when it's calculating Ca-Ca restraints.
I can't find any strange residues in my input file and asking for maximum output from modeller doesn't give me any new information.
I think the problem lies with the second message since I have had the first making earlier models with just a single template and modeller did not stop.
I'll attach a larger chunk of the log file at the end of this message.
Thanks very much in advance for any help.
Daniel Rigden
+-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | http://www.cenargen.embrapa.br | | Asa Norte | Phone: +55 (61)348-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | +-------------------------------------------------------------------------+
TOP______> 159 125 SET RES_TYPES = 'STD'
TOP______> 160 126 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE
TOP______> 161 127 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON
TOP______> 162 128 SET RESTRAINT_GROUP = 9
TOP______> 163 129 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA'
Number of atoms to choose from, total : 4025 4025 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 510 1: 510: Selection residue step (SELECTION_STEP) : 1
selatm___> Number of selected atoms : 510
List of segments of contiguous residues with at least one selected atom:
SEGMENT RNUM AA --- RNUM AA LEN 1 1 SER --- 510 LEU 510
TOP______> 164 130 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA'
Number of atoms to choose from, total : 4025 4025 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 510 1: 510: Selection residue step (SELECTION_STEP) : 1
selatm___> Number of selected atoms : 510
List of segments of contiguous residues with at least one selected atom:
SEGMENT RNUM AA --- RNUM AA LEN 1 1 SER --- 510 LEU 510
TOP______> 165 131 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON'
Restraint type to be calculated: distance iup2crm_E> IUPAC atom not found in topology library: OG iup2crm_E> residue type undefined recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1