On 12/4/11 12:40 PM, Yu Li wrote: > I copy the whole folder > under documents and now the program was able to run. However, I did not > get the pdb file as output. The log file indicate an error occured:
This is obviously complaining that it can't find a PDB file for *input*, not that it can't write the output PDB:
> pdbnam_____E> Filename for PDB code not found: 5fd1 > 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)
Copy the 5fd1 PDB input file into the same folder as your example. Alternatively, copy the atom_files folder (you can find it in the Modeller examples folder) into the same folder that you copied the automodel folder into.
Ben Webb, Modeller Caretaker