When I use my initial model to build the structure, it appears some erros, the
following is the scripts and log file:
...
rdpdb___303E> No atoms were read from the specified input PDB file, since the
starting residue number and/or chain id in MODEL_SEGMENT (or
the alignment file header) was not found;
requested starting position: residue number " ", chain " "
When you provide an initial model, as you have done here, Modeller uses
the information in the alignment file header to read it in. (For
example, your initial model may be a multi-chain crystal structure, of
which you're building only one chain.) So just edit your alignment file
to add a starting residue number - for example, the alignment.ali file
provided in examples/automodel/ has the following header: