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Article ID: 319 - Last Modified: May 9, 2011

Why are structures that have residues ARN, ASH, GLH, LYN, HIE, HIP incorrectly changed to ARG, ASP, GLU, LYS, HIS when converted to PDB?

This feature was deliberately implemented in Suite 2009. Nonstandard residue names such as these have been used as an informal convention to designate different protonation states of regular residues. In order to comply with the official PDB format, the atoms for these residues have to be marked as HETATM or they need to be renamed to standard residues. We chose to do the former.

To preserve the nonstandard names, you can do the conversion from the command line:

$SCHRODINGER/utilities/pdbconvert -imae file.mae -opdb file.pdb -psp

Keywords: PDB, export, convert, protonation, ARN, ASH, GLH, LYN, HIE, HIP, remediated, format, pdbconvert

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