rathankar rao wrote: > i had to model a protein whose ali file, top file and the log files are > present here. i couldnt model it and its always presenting some or the > other errors plz help
The error is: pdbnam__217W> Filename for PDB code not found: 1ocs
This simply means that your PDB file has the wrong name. It should be called 1ocs.pdb or similar (pdb1ocs.ent, 1ocs.atm are also valid names).
> there was one problem in the pdb file,: > a ligand cme under the name of the heteroatom, had a residue number as > 91 , which was supposed to be a number for the aminoacid. the next > residue thus continued from 92 and so on. so i changed the residue > numbers by 1. i changed the ligand atom number also as 1191 instead of > 91 so that it is distinguished from the other aminoacids. despite all > these it dosent work.
There shouldn't be any need to renumber residues in your PDB file. Just make sure you have the correct residue numbering and chain labels in your alignment file.
> i have one more doubt , if at all the protein as many chains then how do > i model it. what is the command which is used to model a protein with > chains.
You don't have to do anything special, although you should separate the sequences for the chains in your alignment file by chain break (/) characters.
Ben Webb, Modeller Caretaker