For example, I want it to show the effects of the element iron on the X enzyme. Does it affect the X enzyme positively or negatively? If it affects, how does it do it, does it disrupt its structure?
Most individual elements will have little to no effect on protein's structure, at least when added in reasonable concentrations. The effect is likely to be seen at a functional level, but for that you need a functional assay rather than a predictive program. For example, adding magnesium to a magnesium-dependent nuclease will not change its overall 3D structure, but it will promote its function.
A general answer to your question is no, though there may be individual exceptions.
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version 2.3.6
I'm way out of my depth here, but maybe molecular dynamics software are relevant to your area.
You created multiple posts on multiple sites for the same question. That is bad etiquette and only serves to annoy people in both communities. Remember you're asking volunteers in two places to spend their time on you while not telling them that you've asked another set of volunteers as well. You're not getting quotes from competing businesses, you're wasting volunteers' time. Please do not repeat this in the future.
Link to cross-post: https://bioinformatics.stackexchange.com/questions/22009/is-there-a-program-that-shows-the-effect-of-an-element-on-another-structure