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Is there a limit on the number of atoms in the ligand that can be used in AutoDock?

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This FAQ applies to: AutoDock 3, AutoDock 4

Is there a limit on the size of the ligand molecule, and if so, how can I change it?
Yes, there is a limit on the number of atoms in the ligand.  By default, the maximum number of atoms is 2048.

This limit is specified in the source code in the file 'constants.h', by the 'MAX_ATOMS' definition:

#define MAX_ATOMS    2048     /* Maximum number of atoms in Small Molecule. */

The path to the constants file is 'autodocksuite-4.0.1/src/autodock-4.0.1/constants.h'.  If you change this line, make sure to change the 'MAX_RECORDS' definition to match the same value as MAX_ATOMS.
by morris last modified 2007-06-26 16:57

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