I am using TS BERNY to optimize the transition state guess structure for my sn2 reaction mechanism. However, when I proceeded to do qst3 calculation, I would receive an error link 9999 all the time. What should I do?
In general, the program failed to localize the TS. I don't use qst3 or qst2, it is much more input preparation to do and it does not have any advantage over opt=ts when you have a good approximation to the TS.
I suggest, what I always do, first to scan the PES:
#P DFT/basis Opt=ModRedundant
0 1
xyz
B 7 21 S 12 0.10
In this example, the bond "B" betwen atoms "7" and "21" is going to be scanned "S" through "12" steps of "0.10" angstroms step size.
Only if you obtain a smooth curve of the scan you'll know you are in the correct pathway, in that case select the structure at the maximum point of the curve and do a TS calculation directly:
#P DFT/basis Opt=(ts,noeigentest,calcfc) freq
If you don't see a smooth curve, then finding the TS becomes readly challenging, or you should look for another way to do the scan PES (other bonds, angles or even dihedrals).
Best, Pablo
When using gaussian16, I faced this error when a batch of inputs were ran in the same directory and then the fort.7 file of them were getting overwritten. There was nothing wrong with the calculation itself, but it did not ended properly because of that. Check the stationary points, if they are truly stationary, maybe is a minor error in finishing (closing) the output files.
This error means that the program did not have enough optimization steps to find the stationary point. Further steps can be as follows:
1. If the optimization is on the right path, then take the resulting "under-optimized geometry" and continue the optimization using opt=ts. But, in my little experience of using qst2 and qst3, this option is extremely doubtful.
2. Therefore, as already mentioned, it is better not to mess with these procedures, but to independently construct the proposed transition state (especially since this is required for qst3) and carry out partial optimization by fixing the geometry of the reaction center. Make sure after optimization that there is only one negative mode left or that the desired mode is significantly different from the others, and only after that start the search for the transition state using opt=ts.
In my experience, despite the apparent complexity, the second way is much faster and less resource-intensive than using qst procedures.
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