Hi,
>Running Modeller8v1 I am getting the following error message: >IOError: openf5__225E> File does not exist: file-not-found >pdbnam__217W> Filename for PDB code not found: adsl.B99990001.pdb > Directories: ./ > Extensions : :.atm:.pdb:.ent:.crd >openf5__224_> Open 11 OLD SEQUENTIAL file-not-found >openf5__225E> File does not exist: file-not-found
Does anyone have a suggestion why it is happening !?
You should take about DOS extensions: rename your file for example (adsl_B99990001.pdb), it should be only one ".pdb" extension. Also make attention for the subdirectory you put the PDB file, env.io.atom_files_directory = './:../atom_files/' Hope this help,
Riadh HAMMAMI UNIVERSITY OF TUNIS EL MANAR, TUNISIA
Hi,
But is modeller who is generating this file adsl.B99990001.pdb. I couldnt find any parameter to set this file name. I just need three files: the script file (mod.py), the align file ( align.ali) and the template structure (1c3c.pdb) The PDB named adsl.B99990001.pdb that modeller cant find is a pdb file generated by it own. as far as I know, modeller generates the models using first the sequence name a putting after it the code B99990001.pdb for the first structure, B99990002.pdb to the second and so on. Modeller generates initials files, but not this one that he couldnt find.
Ricardo.
On 10/10/05, Riadh HAMMAMI riadh.hammami@fst.rnu.tn wrote: > > Hi, > > >Running Modeller8v1 I am getting the following error message: > >IOError: openf5__225E> File does not exist: file-not-found > >pdbnam__217W> Filename for PDB code not found: adsl.B99990001.pdb > > Directories: ./ > > Extensions : :.atm:.pdb:.ent:.crd > >openf5__224_> Open 11 OLD SEQUENTIAL file-not-found > >openf5__225E> File does not exist: file-not-found > > Does anyone have a suggestion why it is happening !? > > You should take about DOS extensions: rename your file for example > (adsl_B99990001.pdb), it should be only one ".pdb" extension. Also make > attention for the subdirectory you put the PDB file, > env.io.atom_files_directory = './:../atom_files/' > Hope this help, > > Riadh HAMMAMI > UNIVERSITY OF TUNIS EL MANAR, TUNISIA > >
-- Ricardo de Paula Nicoluci PhD Student Medicinal Chemistry Laboratory IFSC - University of Sao Paulo Sao Carlos - SP - Brazil
Ricardo Nicoluci wrote: > But is modeller who is generating this file adsl.B99990001.pdb. I > couldnt find any parameter to set this file name. > I just need three files: the script file (mod.py), the align file ( > align.ali) and the template structure (1c3c.pdb) > The PDB named adsl.B99990001.pdb that modeller cant find is a pdb file > generated by it own. as far as I know, modeller generates the models > using first the sequence name a putting after it the code B99990001.pdb > for the first structure, B99990002.pdb to the second and so on. > Modeller generates initials files, but not this one that he couldnt find.
If you send me your input files, I may be able to reproduce the problem here.
Ben Webb, Modeller Caretaker
Hi,
As I tough, the script and modeling run nicely on my pc computer, but on the alpha machine with unix I got that error message. Perhaps it can be due that modifications that you made to able modeller run o Tru64 system. Can you check it from there ?!
Ricardo.
On 10/10/05, Modeller Caretaker modeller-care@salilab.org wrote: > > Ricardo Nicoluci wrote: > > But is modeller who is generating this file adsl.B99990001.pdb. I > > couldnt find any parameter to set this file name. > > I just need three files: the script file (mod.py), the align file ( > > align.ali) and the template structure (1c3c.pdb) > > The PDB named adsl.B99990001.pdb that modeller cant find is a pdb file > > generated by it own. as far as I know, modeller generates the models > > using first the sequence name a putting after it the code B99990001.pdb > > for the first structure, B99990002.pdb to the second and so on. > > Modeller generates initials files, but not this one that he couldnt > find. > > If you send me your input files, I may be able to reproduce the problem > here. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
-- Ricardo de Paula Nicoluci PhD Student Medicinal Chemistry Laboratory IFSC - University of Sao Paulo Sao Carlos - SP - Brazil
-
Modeller Caretaker -
Riadh HAMMAMI -
Ricardo Nicoluci