Is it enzyme dynamics or enzyme kinetics you are talking about? The question is confusing, you are doing SNP detection and wanted to do enzyme "something", does not make much sense directly. Please elaborate what you want to do or what is your project.

I already did generate several enzymes with mutations and did the kinetics yet when I tried to publish my work one reviewer asked me to do enzyme dynamic to estimate the effect of the mutation!?

Hi,

For the enzyme dynamics, you can use chimera structural annotations in which you can mutate the aminoacids. Then in the tools section, define bond parameters to see the changes in H-bondings and clashes. Since, I am not a specialist in this, I refer @Pritam Kumar Panda, a protein structural biologist, who can definitely guide you through the steps.

Best of luck

Now your question makes much sense.

I have few software which you can check if they fulfill your needs. I am not exactly aware of your requirements, but i assume this software might give some help in your project.

http://mmb.irbbarcelona.org/MDWeb/

http://ambermd.org/#AmberTools

https://simtk.org/projects/rnatoolbox

https://ub.cbm.uam.es/software/mmismsa.php

http://futura.usc.edu/software.html

Thank you very much I will check those programs out