hi i am doing ligand modelling in binding site of protein i am using script ligand/multiple-hetero.py as u specified in tutorial but getting error pdb files read when i run script but it shows errors when doing add_restraints that "one or more atoms absent from model" below is the error file after running this script Traceback (most recent call last): File "ligand.txt", line 17, in ? a.make() File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 100, in make self.homcsr(exit_stage) File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 342, in homcsr self.mkhomcsr(aln) File "/usr/local/modeller8v2/modlib/modeller/automodel/automodel.py", line 399, in mkhomcsr self.special_restraints(aln) File "ligand.txt", line 8, in special_restraints rsr.add(atom_ids=ids, restraint_parameters=(2,1,1,22,2,2,0,3.5,0.1)) File "/usr/local/modeller8v2/modlib/modeller/model.py", line 409, in add return self.top.add_restraint('restraints.add', mdl=self.__mdl.modpt, File "/usr/local/modeller8v2/modlib/modeller/util/top.py", line 329, in add_restraint return _modeller.add_restraint(mdl, *args) _modeller.error: add_res_442E> One or more atoms absent from MODEL: N1:101 N3:13 also shown below is log file check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- 95 1 2 113 94 Q S 6.894 204 1 2 222 203 R F 6.290 230 1 2 248 227 P W 7.467 233 1 2 251 230 S V 7.787 END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE read_to_681_> topology.submodel read from topology file: 3 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 19 293 atom names : C +N atom indices : 2385 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 19 293 atom names : C CA +N O atom indices : 2385 2374 0 2386

omgdel__425W> Unselected all O C +N +CA dihedrals: 306 mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. iup2crm_279W> IUPAC atom not found in topology library; residue type index: OD1 2 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom not found in topology library; residue type index: OD2 2 Possible reasons are a non-standard PDB file, or a new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. add_res_442E> One or more atoms absent from MODEL: N1:101 N3:13 please tell me what to do? thank u

Mahendra Eknath Awale Institute Scholar M. S. (Pharm.) Dept.of Pharmacoinformatics National Institute of Pharmaceutical Education and Research NIPER S.A.S.Nagar, Mohali, Punjab-160062 INDIA. Institute Web http://www.niper.gov.in/

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