“Problem in calculating overlap between atoms” error occurred in Point Mutant Scan application

[Anonymous]

Hi all,

I’m trying to run pmut_scan_parallel application with “-score:weights design_hpatch.wts” scoring function, as suggested in manual. However, it always exits from: src/core/scoring/sasa.cc line 215 and an error reported:

“Problem in calculating overlap between atoms. Termination calculation.
radius_a: 3.16, radius_b: 3.16, distance_ijxyz: 14.199, cosine theta: 2.245″

Does it mean that atom a and b are too far from each other so that there is no overlap between them? Why it happens in hpatch scoring, and any suggestion to avoid it?

Many thanks,

xfliu

[Anonymous]

It looks like your interpretation is correct. I’ve sent out a query for more details. It would help if you could provide an input file that causes the error.

[Anonymous]

Thanks a lot Lewis! This error occurs for a variety of pdb files I tried. So I do not think it is likely the problem of input files. Anyway, thank you for forwarding this problem to the right person.

[Anonymous]

I have located someone who knows an answer, but it will require patching your code. He said he’ll reply here when he is able.

[Anonymous]

This got fixed…I’d guess it will get released when we go to weekly releases in two months or less. I can try to make you a patch if you’re still interested. https://carbon.structbio.vanderbilt.edu/mantisbt/view.php?id=29#c139

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