On 07/06/2011 06:58 AM, MUSTAFA BUGHIO wrote: > I am trying to do energy minimization step by running optimize.py script > file but it does not execute every time i tried to run and got the > following error, i will be thankful if you help me get this problem > resolved. > > IOError: pdbnam_____E> Filename for PDB code not found: hGLR > Directories: ../atom_files > Extensions : :.atm:.pdb:.ent:.crd > (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, > .7z, .xz, > and trying PDB-style subdirectories - e.g. ab for > pdb1abc.ent)
Just like it says, you asked it to open a PDB file called "hGLR" and told it to look for it in the ../atom_files directory, and it can't find it in there. Set env.io.atom_files_directory to the directory containing your PDB file (or remove that line entirely if it's in the same directory as the script).
Ben Webb, Modeller Caretaker