AUTOBUILD and AUTOBUILD-LX

AUTOBUILD is a Fortran program which allows the construction of large numbers of chemical structures in INTERCHEM format. These structures are suitable for use by the program THREEDOM, and as starting structures for quantum-mechanics calculations using MOPAC.

Structures are formed by attaching from one to four fragments to a template structure.

The program comes complete with several fragment libraries; while these are meant to serve as examples, but can also be used in real drug design schemes. The fragment and template structures are held in modified INTERCHEM format files, and can be made using the program INTERCHEM.

The use of the program is best illustrated by an example:-

It is required to make structures for pyridine derivatives with substituents on positions 2, 3, and 6 on the pyridine ring; the range of substituents being identical for all the substituent positions and being limited to; hydrogen, methyl, ethyl, and isopropyl. There are four basic steps.

1. The template structure is obtained using INTERCHEM from the standard pyridine structure in the INTERCHEM catalogue, the three substituent positions being appropriately selected. This structure is deposited in a file (called for example:- pyrtempd.DAT).
2. The four necessary fragments are copied from the AUTOBUILD fragment directories and placed in a new empty directory (called for example:- fragdir).
3. The program AUTOBUILD is started; entries for the filename root and suffix are typed in (for example ABC and DAT )
4. When prompted the names of the template structure (pyrtempd.DAT) and fragment directory (fragdir) are entered; in this case there will be three calls for entry of the same directory name.

The program will proceed to construct all of the 64 ( i.e. 4 x 4 x 4) structures. Each structure will be optimized using the molecular mechanics program ICMECH and stored as one of a series of sequentially numbered files called (for the example chosen) ABC0001.DAT to ABC0064.DAT.

Fully optimized structures (of size appropriate for the example above) can be made at the rate of about 14 per minute. It optimization is not required the rate can approach 400 per minute.

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Revised 18th June 2007