Luis & all Modellers -
OK, now that you've 'fixed' your problem, I think I've seen this before as well. In my case, it happened when I had moved my template PDB files from a PC to my SGI system, and MODELLER did not like the DOS format of the files. With nedit, if you open the file and then click "File" and "Save As", it will have a checkmark by MS-DOS Format if that is the case. Simply click that option OFF and save the file to remove the DOS formatting.
PS - I'm still curious about a simple way to set up an MD annealing run on a final model without any remaining restraints from the template. Can the developers point me to an example or guidelines in the manual?
Thanks & Happy Modelling,
Tom -- Thomas M Duncan Research Associate Professor Dept Biochemistry & Molecular Biology Institute for Human Performance, Rm 4311 SUNY Upstate Medical University 750 E Adams St Syracuse, NY 13210