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"
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