Knowledge Base

Article ID: 1106 - Last Modified: June 2, 2011

My loop sampling job did not give any results. What can I do?

Sometimes loops are in tight locations and it may be difficult to find reasonable conformations during the sampling routines. In these cases, it may help to modify the default settings for the loop sampling:

The Options panel, available from the Prime refinement panel, includes the possibility of setting different values for the vdW overlap and C-alpha movement. Lowering the vdW overlap will often aid in finding loops.

Other possibilities are to perform a minimization on the loop before starting the loop sampling job or try a different loop sampling method; e.g., if the job that produced no output was run with an Extended sampling protocol, try using the Default sampling instead.

Keywords: Prime, loop prediction, loop placement, job died, job failed

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