I am trying to use rosetta3.1 cluster function to cluster 1000 pdbs of a homodimer that were created by Symmdock of rosetta3.2 and are still in centroid mode. Even if I get the pdb outputs for the clusters , I still get an output txt file that crashes at line 2,707,992 and doesn't give me the clustering information. The problem is that there are so many warning messages of the following types for each atom:
core.conformation.Conformation: [ WARNING ] missing heavyatom...
core.io.pdb.file_data: [ WARNING ] can't find atom for res 84 atom CEN...
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 517 in file...
that the output file crashes before it gets to the clustering information.
I know that my command line works since when I try it on say 20 structures it works just fine in outputing both the warnings and the clustering information.
I thought maybe it will help if I silence all the warnings so it won't print them to the output file so it will have room to print my clustering information. Is it even possible? if so,how?
If not, can anybody tell me how to fix this problem so it will print out my clustering information to the txt output?
Thank you very much,