vidhya sankar wrote:
1) WHEN I RUN SUPEPOSE.py script i have got the follwing warninig
how can i rectify
readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 8
Modeller will only read the first 80 characters of this line.
Your PDB files are not valid PDB file format. See http://www.wwpdb.org/documentation/format23/sect1.html - in particular see under "Record Format": "Each line in the PDB entry file consists of 80 columns". Thus Modeller only reads the first 80 columns, and ignores anything else you may have.
2)WHEN I RUN model_evaluate.py i have got the follwing warninig how can
i rectify
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 5 529
atom names : C CA +N O
atom indices : 4234 4226 0 4235
This warning is harmless. When building models using CHARMM topology, certain bonds, angles, and (in this case) dihedrals are constructed between each amino acid residue and the next one in the sequence. For your last (C terminal) residue, there is of course no next residue, so it can't build the bond, angle or dihedral.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage