Dear Doctors and Modeller users,
We are graduate students in Fortaleza, Brazil and we are trying to model an aminoacid sequence deduced from genotyping data using the MODELLER for Linux (RedHat 9.0)! Thus, we would like to know if you could help us on the script for modelling our target sequence, cause we are having some troubles with that. Our log output file stops after the CHECK_ALIGNMENT, in the BEGINNING OF COMMAND, telling us the template's structure had not been read. We put our atomic coordenates files (1uw3.atm and pdb1uw3.ent) into the /examples/atom_files/ subdirectory.
Another error message appears when we put, in alignment file (pri.ali), "structure" and "sequence" in front of the template and target sequence respectively. This error message is "rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files/pdb1uw3.ent"
Please check our *.top *.ali and *.log files attached.
We would appreciate very much if you could give us some light on solving this problem. Beforehand I thank you for your attention...
Vasconcelos, EJR and Nugen (Núcleo de Genômica e Bioinformática) Group - Fortaleza, Brazil