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

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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