Hi, I'm trying to group structures into clusters, but I have an error and an empty log file. A few months ago (in February / March) I didn't have a problem with it, although I did it in the same way (I think so). I have no idea where this problem comes from.
Using the AbinitioRelax protocol, I obtained a silent file with 100,000 structures (centroid representations) for a certain amino acid sequence. Now I want to group the structures into clusters and sort by energy. I use the following commands:
. /home/bioinf/PATHS.sh (path to rosetta databases)
cluster @cluster_options > cluster.log
where the file cluster_options looks like:
and here I only get the message "Can't open @cluster_options" and an empty file cluster.log (this is probably not a problem with permissions to cluster_options file because everyone has full rights (-rwxrwxrwx)).
I also tried to write options with the command. I used the command:
cluster -in:file:silent ../silent_file.out -cluster:sort_groups_by_energy -cluster:radius 3 > cluster.log
and here I get:
option -i unrecognized - ignored
Usage: cluster <options> graphfile
-C k - generate no more than k clusters (0)
0 : no limit
-c k - use clustering method k (0)
0 : use modularity
1 : use modularity quality
-o <outfile> - output file (stdout)
-v - verbose mode
-? - print usage
Can you help me? Please. I have been tired of it for several weeks and I still can't see why I'm failing now, although a few months ago everything worked well. However, I don't know Rosetta very well, I just use what I learned in college and what I found on www.rosettacommons.org.
I look forward to your reply.