Hi, I am using Rosetta to relax a enzyme with a substrate and a cofactor. The "flags2" was from rosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs
The params file for substrate (DHD.params) and cofactor (NAP) were also used.
But errors!! How to solve this problem?
"flag2" was scucessfull for the "1A99_1A99.pdb" inrosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs
(base) ubun@ubun-System-Product-Name:~/relax/test$ $ROSETTA/main/source/bin/relax.mpi.linuxgccrelease -s 01-MD-086DS.pdb @flags2 > log2.txt
[ ERROR ]: Caught exception:
File: src/core/id/NamedAtomID_Map.hh:390
Residue outside res_map range
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------
| Attachment | Size |
|---|---|
 01-MD-086DS.pdb | 440.28 KB |
 DHD.params | 4.11 KB |
| flags2 | 321 bytes |
It's a bit hard to say without seeing the contents of the ROSETTA_CRASH.log file (specifically the backtrace that's printed there).
I will note that Rosetta isn't necessarily written to be robust to Unicode, so one thing I would try is to remove all the non ASCII characters from the flag file and see if that helps. (I doubt it, especially as you said it worked with the other file, but it's worth a trouble-shooting step.)