My Prime loop sampling job fails with the following error message:

ERROR: No valid structure conformations were found.

Is there anything I can do to make Prime sample my loop?

If this is a default loop sampling job, you can try to decrease the "Minimum distance: [ ] of vdW radii" setting in the Options dialog box of the GUI. This change will allow a closer overlap between atoms in the loop search and should, in most cases, allow a loop to be built.

Alternatively, you could consider adding in a residue from one or both end points of the loop to allow a larger search space for the job.

For extended loop sampling jobs, similar approaches can be tried.

You can allow a little more vdW overlap of atoms in the initial stages of the job. By default, the following three overlap factors are used:

0.65/0.70/0.75

and you may want to try to lower that to either 0.60/0.65/0.70 or 0.55/0.60/0.65 which will allow for somewhat closer contact between atoms in the initial loop sampling stages.

In order to do this, you will have to add the following line to your input file:

OFAC_INIT_STAGE 0.60/0.65/0.7

or

OFAC_INIT_STAGE 0.55/0.60/0.65

Then start the job from command line:

$SCHRODINGER/prime jobname.inp

You may also consider lowering the overall allowed overlap factor, that by default is set to:

MIN_OVERLAP 0.70

These keyword are explained in the Prime User Manual, section 10.2.

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