I am trying to get RECON multistate Design going and have run into an issue. I have made my RECON xml script and a bash script:
<ScoreFunction name="ref15" weights="ref2015" />
<SeqprofConsensus name="pssm" filename="pssm.txt"
<InitializeFromCommandline name="ifcl" />
<ReadResfile name="resfile" filename="resfile.txt"/>
<PackRotamersMover name="design" scorefxn="ref15" task_operations="pssm,ifcl"/>
<MSDMover name="msd1" design_mover="design" constraint_weight="0.5" resfiles="resfile" debug="1" />
<MSDMover name="msd2" design_mover="design" constraint_weight="1.0" resfiles="resfile" debug="1" />
<MSDMover name="msd3" design_mover="design" constraint_weight="1.5" resfiles="resfile" debug="1" />
<MSDMover name="msd4" design_mover="design" constraint_weight="2.0" resfiles="resfile" debug="1" />
<FindConsensusSequence name="finish" scorefxn="ref15" resfiles="resfile" task_operations="ifcl,pssm" />
<FastRelax name="relax" task_operations="ifcl" scorefxn="ref15"/>
<FitnessFilter name="fitness" output_to_scorefile="1" />
<Add mover="msd1" />
<Add mover="msd2" />
<OUTPUT scorefxn="ref15" />
The command line options here are:
##NESSARY JOB SPECIFICATIONS
#SBATCH --job-name=JobExample1 #Set the job name to "JobExample1"
#SBATCH --time=00:30:00 #Set the wall clock limit to 1hr and 30min
#SBATCH --nodes=1 #Max 4 Nodes
#SBATCH --ntasks-per-node=16 #Max 28 Tasks Per Node
#SBATCH --mem=16G #Max 32 GB Per Node
#SBATCH --output=Out.%j #Send stdout/err to "Out.[jobID]"
module load Rosetta/3.13-foss-2018b-Python-2.7.15
module load OpenMPI/4.1.1-GCC-11.2.0
mpirun -np 2 /sw/eb/sw/Rosetta/3.13-foss-2018b-Python-2.7.15/bin/recon.mpi.linuxgccrelease -database /sw/eb/sw/Rosetta/3.13-foss-2018b-Python-2.7.15/database -s elevator.pdb elevator_cis.pdb -in:file:fullatom -out:file:fullatom -use_input_sc -parser:protocol MSDesign.xml -nstruct 1 -extra_res_fa retinal_no_oxygen.params -resfile resfile.txt
When I run the script I get this ROSETTACRASH error message:
[ ERROR ] UtilityExitException
ERROR: Cannot open file resfile
So I have tried a few things like removing (filename="resfile.txt") from my recon script to see if I could override it from commandline. I have also removed the commandline option -resfile resfile.txt. I also have used several older resfiles which worked in different runs so I know the resfile is in proper rosetta format. I am stumped. Any help would be greatly appreciated.
First off, for RECON you need to have one resfile per state, separated by commas. Right now you only have a single resfile designated (with `resfiles="resfile"`).
When you specify your resfile, you need to specify the full name of the resfile, including extension. If your resfile is named "resfile.txt", you would need to specify `resfiles="resfile.txt,...."`. As a general rule, Rosetta doesn't have any implicit understanding of extensions, so in almost every case you need to specify the full name of files, including the extension. If you leave it off, Rosetta will look for a file which is just "resfile", without an extension. (The error message "cannot open" is usually due to file naming or file path issues, rather than file content issues.)
By the way, if you're looking for more info on the RECON protocol, portion of the Protein Design tutorial for the Meiler Lab Workshop focuses on RECON. See http://csb.vanderbilt.edu/workshops/rosetta_aug2020/materials/index.php and https://www.youtube.com/playlist?list=PLYuStm_BniykhlMFAus-UEwR-_qmAVWsK for more info.
Hey rmoretti thank you for your quick response! When I return to lab after weekend I will try out those suggestions and let you know how they go.
and just to specify now, you're saying
1: create a unique resfile for each of the states (2 in this case)
2: in the ReadResfile task operation I need to list each one comma separated.
3 make no changes to the MSDmover where the resfile identifies stays the same.
Thank you again for your help. I tried out your suggestions one by one and found the issue. The first thing I tried was to go into the resfile tag within the MSD mover itself and add the ".txt" identifier to the end of my resfile name and sure enough it started working!
Thank you again