I currently have two questions.
The first related to using the relax.linuxgccrelease,
I am relaxing a cleaned native structure to produce a 1000 decoys, in which I will cluster and use the top 5 to perform docking with Rosetta.
My question is when I relax my native structure, what options and flags should I include and not include. Should I be relaxing with contraints on the main chain and side chains, or should I relax with no constraints. Should I include -ex1 and -ex2aro flags for my purpose? Should I perform relax:fast or relax:thorough?
My next questions pertains to running the cluster_vs_rmsd.py script. I have tried to run it by ./score_vs_rmsd.py --native /home/ralphkfoury/projects/singaporeProject/structures/cleanstructures/1ATNcleanedAD.pdb --table=1atnscorevsrmsd.pdb --term=total /home/ralphkfoury/projects/singaporeProject/dockings/knownenergydockings/ActinvsDeoxyribonuclease1ATNchAD/clusterlogsandtextfiles/Dockingoutputstructureslist.txt
It keeps showing an error this error,
File "./score_vs_rmsd.py", line 43, in <module>
rms = pdbStat.calculate_rms(native,decoy,options.ca,options.residues,"",options.chain)
TypeError: calculate_rms() takes exactly 8 arguments (6 given)
Can anyone help me figure this out?