Frederico,

Does your ali file segment matches one in PDB file? If you have chain A in PDB file, and don't specify that in ali file, and top file, you might get in trouble. Add MODEL-SEGMENT in your top, make sure it is in PDB file and in the second line of an ali file.

Check the manual for more details...

I hope this helps, Bozidar

On Thu, 18 Jul 2002, Frederico Moreno wrote:

> Hi, > > I'm using a correct pdb files. I got this message > below. What's wrong? > > openf5__224_> Open 11 OLD SEQUENTIAL > /home/pepeu/Modeller/modeller6v2/examples/Lectin/1h9p.pdb > rdpdb___303E> No atoms were read from the specified > input PDB file: > 1) Possibly because an > incorrect/non-existent PDB file is specified. > 2) Possibly because the segment is > specified incorrectly in the > alignment file or by the TOP > variable MODEL_SEGMENT. That is, > the beginning residue number and/or > chain id in MODEL_SEGMENT > may not be found in the input PDB > file; MODEL_SEGMENT: 1: > To find out more, switch on maximal > output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' > rdabrk__288W> Protein not accepted: 1 > rdabrk__290E> Number of residues in the alignment and > pdb files are different: 237 0 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 > 1 > > Moreno > > _______________________________________________________________________ > Yahoo! Encontros > O lugar certo para encontrar a sua alma gêmea. > http://br.encontros.yahoo.com/ >