The fixdupatomnames utility helps prepare input files for use with programs such as reduce that expect each atom in a residue to have a distinct name. It will identify and rename atoms that have the same name as a previously seen atom. Residue numbers for small molecules may also be altered. See the Tutorial and chapter mkhetdict for more information about reduce.


If you have structure files with residues having duplicate atom names (not common but some workflows create files like this) and you want to run reduce or another program that expects unique atom names, fixdupatomnames should be used before running mkhetdict or reduce.

> fixdupatomnames mol.mol2 mol-renamed.pdb
> mkhetdict mol-renamed.pdb mol_hetdict.txt
> reduce -db mol-hetdict.txt -build -rotexist mol-renamed.pdb >molH.pdb

Command Line Interface

A description of the basic command line interface can be obtained by executing fixdupatomnames with no arguments.

prompt> fixdupatomnames

will generate output similar to the following:

  fixdupatomnames, Copyright (c) 2010-2015
  OpenEye Scientific Software, Inc.
  Version: 1.2.1
  Release: 20150305
  OEChem version: 1.9.2 20150305
  Platform: redhat-RHEL5-g++4.1-x64

  Licensed for the exclusive use of Company Name.
  Licensed for use only in Site.
  License expires on August 15, 2015.

No arguments specified on the command line
Required parameters:
    -input_mol : Input molecule file.
For more help type:
  fixdupatomnames --help

Required Parameters

-input_mol <filename>
-i <filename>

[keyless parameter 1]

Input molecule file.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz
-output_mol <filename>
-o <filename>

[keyless parameter 2]

Output molecule file. Duplicate atom names within a residue will be changed.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz


If the file is to be used with reduce, then the extension .pdb is required.

Command Line Options

Other Options

Print additional information to standard-error.

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