Greetings !
I am using a local installation of I-TASSER4.1 and am experiencing two errors at the "3.2 make restraints" stage of "runI-TASSER.pl" . In the output I either have :
( 1 ) many "CYS ne GLY" or "GLY ne CYS" errors or
( 2 ) one obvious "XXX ne 1" error accompanied by errors enough to account for the entire alignment length.
The source of the first problem is hard for me to identify. The code will complain either about a GLY needing to be a CYS or vice versa. When I "grep out" the CYS/GLY it is complaining about, it is sometimes the case that there actually is a GLY/CYS aligned but other times there is no GLY/CYS. In other words, sometimes the identified discrepancy doesn't exist in the "init.dat" file and other times it does.
The second problem is easy to spot. Upon opening the "init.dat" file I observe the following suspicious line :
...
ATOM 1139 CA VAL 139 86.000 40.415 23.897 139 VAL
ATOM 1140 CA 1 140 87.546 39.491 30.471 140 HIS
ATOM 1141 CA HIS 141 90.679 40.489 28.583 141 GLY
...
Any thoughts on how a "1" could have snuck in to the code as a three-letter residue code ?
Could this have thrown off the alignment and resulted in the many, many other errors ?
So far, as remedy, I have attempted to initiate "runI-TASSER.pl" after the errors to see if the step that had failed could be re-run with success. I have also gone as far as starting from the 'seq.fasta' stage ( i.e. restarting the whole process ). Both of these strategies have resulted in the same errors.
Attached are some representative "init.dat" and accompanying output files documenting these errors.
Please let me know if there is anything else I can provide.
Cheers,
tim