TURBOMOLE Users Forum

Forum General => Miscellaneous => Topic started by: hmsenn on August 04, 2007, 04:57:57 PM

Title: UFF atom types
Post by: hmsenn on August 04, 2007, 04:57:57 PM

Dear all
I find Turbomole's UFF module very useful to preoptimize largish organic molecules (~300 atoms). However, the automatic atom-type assignments are not always correct, which can lead to locally heavily distorted geometries (e.g., pyramidalized atoms in aromatic ring systems).
So my question is if there is a way to set the atom types manually. Other things like bond orders or the connectivity can be adjusted in the ufftopology file. However, I haven't found a way to access the atom types.

Best wishes
Hans

Title: Re: UFF atom types
Post by: uwe on August 07, 2007, 05:21:14 PM

Hi Hans,

if you name the atoms in the coord file like the uff-types, uff will recognize them.

So if you have in the coord file something like:

0 0 0 c

and uff tells you that this is of c_3 type, then you can change it to, say, c_r by changing coord to:

0 0 0 c_r

or, better:

0 0 0 c r

because the other Turbomole modules will just ignore the 'r'.

Regards,

Uwe