Member Site Forums Rosetta 3 Rosetta 3 – General Loop modeling FLAGS Reply To: Loop modeling FLAGS


    Thank very much! It is already working!!

    > Hello, I would like to ask about loop modelling flags.
    > I am modelling a loop using the following flags file:
    > -nstruct 500
    > -database /data/jklett/Software/src/rosetta3_databa
    > -in::file::fulllatom
    > -loops::input_pdb t000/t000.template.pdb
    > -loops::loop_file t000/t000.pose_loops
    > -loops::frag_sizes 9 3
    > -loops::frag_files t000/aat000_09_05.200_v1_3 t000/aat000_03_05.200_v1_3
    > -loops::build_initial false
    > -loops::remodel quick_ccd
    > -loops::refine refine_ccd
    > I am trying to run this model in a cluster, and to do so, I submit the following script:
    > #!/bin/tcsh
    > $EXEHOME/rosetta3-bin/32/loopmodel.linuxiccrelease @flags
    > as many times as the numbers of processors I want to use.
    > My problem is that when i send this script 80 times (80 processors), it takes ages to get my results. In average, I get about four models every half an hour. I don’t know whether I am not writing the appropriate flags.
    > thanks very much in advance