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CHNG a b c d e

CHNG must be followed by five integers. The first two are atom numbers. The first atom is the point of attachment of the sidechain, and will remain unchanged. The second atom will be changed into the side chain.

The third number (c) is the index of the sidechain that will be introduced. These are found in the file sdchns.dat in the local directory. The default version contains the following:

        1       Hydrogen
        2       Methyl
        3       Hydroxy
        4       Phenyl
        5       Cyclohexyl (equatorial connection)
        6       Cyclohexyl (axial connection)
        7       Ethyl
        8       Trimethylsilyl
        9       t-Butyldimethylsilyl
        10      Benzyl
        11      t-Butyl
        12      R-thp
        13      S-thp
The fourth integer was unused in version 0.9 and was set to 0. In version 0.91 this integer controls the approximate optimisation of the sidechain orientation. If it is 0, optimisation is not used. If it is 1, the original optimisation algorithm is employed.

The final integer (e) is set to zero if a substructure minimisation is not required and to one if it is. If it is set to one, then there must be a SBCF command somewhere in the command file. If the substructure file is not empty, then its contents will be read and new numbers appended. This option creates a substructure constraint file which fixes the positions of all atoms in the structure, except those of the new side chains. A substructure minimisation will then optimise the sidechain without affecting the main structure. This does not appear to be very useful.

Setting up new sidechains:

Create new structure in MacroModel with the new atom a as atom number 1 and b as atom number 2. Minimize. Delete all other atoms connected to the new a atom. Save structure. Edit structure file. Remove the title. Copy the contents of the structure file to the bottom of the file sdchns.dat.
Acca and Acca documentation: © 1996,1997 J M Goodman, Cambridge.
Acca documentation may not be copied without the written permission of the author.

© Goodman Group, 2005-2017; privacy; last updated October 19, 2017

department of chemistry University of Cambridge