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Article ID: 360 - Last Modified: June 6, 2011

Optimizing the H-bond assignment results in an error like:

File "schrodinger\protein\assignment.py", line 449, in enumerate_states
if ct.measure( iatom, iacceptor ) < 2.0:
File"schrodinger\structure.py", line 3162, in measure self.handle, atom2)
TypeError: an integer is required

What is going wrong?

This error typically means that there is some problem detecting the appropriate atoms during enumeration of the possible states of a residue, probably because the PDB atom names are incorrect or inconsistent (e.g., a mix of remediated and unremediated names) or the residue has covalent modifications. Usually, simply deleting all hydrogens (via the "X" button on the toolbar) and adding them back again will solve the problem. The Preprocess step of the Protein Preparation Wizard will add hydrogens back to the structure with the expected PDB names, or you could use the Add hydrogens toolbar button to add back the hydrogens.

Keywords: protein preparation, hydrogen bond assignment, TypeError, PDB atom name

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