Subject: MOPAC dummy atoms

From: "Ratty" <[email-masked]>
Date: Fri, 30 Aug 1996 12:47:47 +0100 (BST)

I am trying to model the effects of Methyl groups on a molecule using mopac,
by comparing whole molecules with those with certain methyl groups missing.
I already have z-matrices for the complete molecule, however I am having
problems with removing methyl groups. The way I am doing this is 'commenting
out' the relevent methyl groups as follows.

M-CH3 becomes
M-HX3 
where X refers to a dummy atom.

On substution the M-C distance is 1.5 A and the M-H distance is 1.1 A the
bond angles and dihedral angles remain the same

This however doesn't appear to work. The hydrogens that replace the methyl
carbons do not appear in the 'right' place. When running the job in mopac it
complains that atoms are too close to each other or in straight lines. Also
when examing the file using RasMol it appears that the hydrogens are in the
same position as the atom they are supposed to be bonded to (i.e. the bond
length is 0 not 1.1 A as specified)

Does anyone know what I might be doing wrong,

Cheers
Ratty