From m10!frisch@uunet.UU.NET  Thu Dec 24 11:42:44 1992
Message-Id: <9212242144.AA10317@relay1.UU.NET>
Date: Thu, 24 Dec 92 16:42:44 EST
From: m10!frisch@uunet.UU.NET (Michael Frisch)
Subject: Re: Newzmat: from xyz to z-matrix
To: uunet!obelix.cica.es!rafapa@uunet.UU.NET, chemistry@ccl.net


    >X-Envelope-to: chemistry@ccl.net
    
    	I am trying to convert from cartesian coordinates to z-matrix
    format suitable for Gaussian92 using the newzmat program. I want to have
    a few dummy atoms in the final z-matrix so I have been trying to use the
    -tzmat option to give a template z-matrix. Whatever I try the program
    always finish with an Link1 error message. Somebody knows if the use of
    dummy atoms is not possible in the template z-matrix?
    thanks in advance
    
    		Dr. Rafael R. Pappalardo
    		Dept. Physical Chemistry
    		Univ. de Sevilla (SPAIN)
    		e-mail:rafapa@obelix.cica.es
    
Template z-matrices don't work very well in NewZMat.  The usual trick
for adding dummy atoms is:

1.  Add the dummy atoms to the cartesian coordinates as some type of atom
    that isn't in your molecule -- U is usually a good choice.  These should
    be placed so as not to break any symmetry the molecule has, but this is
    normally what is needed with dummy atoms, anyway.

    Of course, if your cartesian coordinates come from some graphics program,
    you'll just draw the dummy (U) atoms in (after any mechanics
    minimization, of course).

2.  Run NewZMat with the -allbonded keyword so that the "dummy" atoms
    can be used (i.e., the z-matrix connectivity can be defined) however
    NewZMat sees fit.

3.  Edit the resulting z-matrix and changed the U's to X's.  Be careful
    to move variables defining the dummy atom positions to the constants
    section of the z-matrix, and then use the FOPT keyword on the route
    card to double-check that you have arrived at the correct number of
    variables are left.
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