Hello everybody,

please find enclosed two updated scripts which effectively do the same but with different inputs. In the original post the sequence how product and TS were written was simply wrong.

Quite likely they can be merged into one but for the time being I kept them separate.

Both use 3 structures to generate the input for a DMol^3 TS Conf run. This might be of interest when you have a set of different reactants, products, and transition states and if you want to see via a TS Conf run how they are connected to each other.

Script 1 in mk-R-P-TS-ARC from TS Conf Script.zip
Uses 3 frames in a trajectory of a TS Conf run to generate the input file for the TS Conf run.

Script 2 in mk-R-P-TS-ARCv3 Script.zip
Writes assumed reactant, transition state, product (as *.xsd files) into an arc file which can be used in a TS Confirmation run. These can be the optimized (TS Search and Geometry Optimization) structures of a TS Confirmation run. Please keep in mind that all atoms might be matched properly already.

So far I do not have a unique procedure to guarantee this always is the case for arbitrary systems (the formula of course always has to be the same) and you may have to generate the matches using the reaction preview functionality for all possible 2-tuples of reactant, transition state, and product to make sure that all have the same match. The first frame and the last frame of the resulting reaction previews are the structures which can be used in this script. As there are 3 possible matches altogether I am not sure if this always lead to usable input files.

Please let me know if you find any problems and/or rate the script if you find it use full.

Kind regards,

Carsten Menke