Dear Rosetta community,
I went over the antibody structure prediction tutorials and now in the process of modeling structures for my custom sequence which has 27 aa’s in the CDRH3. When I ran the following command,
antibody.linuxgccrelease -fasta cfab.fasta
I got the following error
[ ERROR ]: Caught exception:
File: src/basic/execute.cc:78
[ ERROR ] UtilityExitException
ERROR: basic.execute encounter error while runnning blastp [-db, /n/karplus_lab/aravinda1879/software/rosetta_bin_linux_2020.50.61505_bundle/main/database/additional_protocol_data/antibody//blast_database/database.H3.27, -query, grafting/h3.fasta, -out, grafting/h3.align, -word_size, 2, -outfmt, 7, -max_target_seqs, 1024, -evalue, 2000, -matrix, PAM30]
BLAST Database error: No alias or index file found for protein database [/n/karplus_lab/aravinda1879/software/rosetta_bin_linux_2020.50.61505_bundle/main/database/additional_protocol_data/antibody//blast_database/database.H3.27] in search path [/n/holyscratch01/karplus_lab/aravinda1879/rosetta_work/mmp14/cfab::]
Exiting...
According to the error, blast fails to look for the sequence database with 27 aa’s. And I understand that this is true since there are no DB with 27 aa’s for CDR H3 region. Can you kindly direct me towards possible options I have?. I tried looking for some camelid like antibody modeling tutorials. But I did not find any except of r the information on this webpage.
https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-mode-camelid
However, I am not sure where the files mentioned on this page located. For instance, I could not find the following file anywhere in my installation directory. I am using rosetta_bin_linux_2020.50.61505_bundle
Thanks in advance.
~/antibody/scripts/rampaths.txt
.
