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Re: Problem with internal coordinates

Pedro Silva
pedros@ufp.edu.pt


IZMAT input includes a number defining the type of coordinate (1 means bond, 2 means angle, 3 means dihedral, etc., as described in INPUT.DOC), followed by the numbers of the atoms involved in that coordinate. Therefore, the lines you mention:

izmat(1)=
1,1,2,
2,1,2,3,
1,2,3


mean:
a bond between atoms 1 and 2
the angle defined by atoms 1,2,3
a bond bewteen atoms 2,3

If you had a larger molecule and wanted to include a dihedral with atoms 4,3,2,1, you would add:

3, 4,3,2,1

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