FW: Hanging on PDB file

[kristen.browne@…]

Sorry sent this to the admin by accident!

This is another workflow that is repeatedly hanging.

I'm not 100% as to what it is doing when the hang starts (but you do have my email address!)

K

Kristen Browne, MSc, MscBMC
Contractor - MSC, Inc. | A Guidehouse Company
3D Modeling and Biovisualization Specialist
Bioinformatics and Computational Biosciences Branch (BCBB)<https://www.niaid.nih.gov/research/bioinformatics-computational-biosciences-branch>
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1fvm-monomer-blue.pdb​

logs (8).txt​

[kristen.browne@…]

Added by email2trac

[kristen.browne@…]

Added by email2trac

[pett]

Hi Kristen,

The problem here is that the semi-empirical sqm program that ChimeraX uses to determine partial charges in non-standard parts of structures can take a very long time for some moieties, particularly larger ones like this, with the fact that it forms a large ring possibly a contributing factor. It can also fail for some moieties, notably ones with significant negative charge concentrations (e.g. multiple phosphates).
I've been running coulombic/sqm on this entry for over 26 CPU hours, so who know if it would ever finish. There is an alternative charging method, "gasteiger", which is less accurate than sqm but which always finishes within a few seconds -- but which has its own set of (different) failure modes. Let me know if you want me to change the preset to that method.

--Eric