(Modeling proteins)

Protein Intrinsic Reaction Coordinates


The final step in validating a transition state in an enzyme-catalyzed mechanism is to check that the candidate transition state does, in fact, connect the two stable intermediates it's supposed to connect.

Verifying that the transition state is for the intended reaction

At this point, a FORCETS calculation should have been done, and a restart file written using ISOTOPE. If this has not been done, do it.  Assuming a restart file now exists, proceed as follows:

Copy the FORCETS data-set to create a new data set.  A suitable name would be Step_1_2_IRC.mop.  Copy the FORCETS restart file as well, i.e., to give Step_1_2_IRC.res

Edit the data set to replace FORCETS ISOTOPE with IRC=1* RESTART X-PRIORITY=0.05 EPS=78.4 CYCLES=100 Run the job.  It will produce several files.  The file ending in .xyz is suitable for mapping using JSmol.  Examine the animation of this file using JSmol or other GUI, and if the start of the animation is the reactant and the end of the animation is the product, then the IRC is correct.  If the animation is backwards, that is if the reactants and products are swapped around, re-run using IRC=-1*   If the reaction is not complete, increase the size of nn in CYCLES=nn.

If everything works, go out and celebrate.