Dear Stephane be sure that the PDB file exist and it has coordinates for exactly the same sequence that you are using in your alignment file. This latter seems to be your problem. best wishes, Andras govind@bic.nus.edu.sg wrote: > > Dear All, > > When I exectute the top command file, its not running the modeller. Its > reporting the following errors. Please clarify my doubts. > > Thanks in advance > govind. > > ipdbnam_W> environment variable PBNET undefined > > >> CHECK_ALIGNMENT: > > rdpdb___E> no atoms read from the input PDB file; > probably because segment specified incorrectly in the alignment file or in > MODEL_SEGMENT; > beginning residues number/chain id probably not found: 1 > chkseq__E> Number of residues in the alignment and pdb files for alignment > entry: 1 > fndatmi_E> residue atom index out of bounds; ****** -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras