I have developed a 3D model of protein structure and minimized its energy through two different tools. After model refinement, I have checked energies of my models, obtained from two different tools. Interestingly, both models have shown a different type of structure after energy minimization and refinement. Why it so? I am a bit confused about it?
There are even more tools than you have found, some of them are below.
The first post shows that there is no right or wrong answer...
"ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model.
Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field.
ModRefiner has an option to allow for the assignment of a second structure which will be used as a reference to which the refinement simulations are driven.
One aim of ModRefiner is to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology and side-chain positioning.
It also generates significant improvement in physical quality of local structures. The standalone program also supports ab initio full-atomic relaxation, where the refined model is not restrainted by the initial model or the reference model."
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K Proteins. 2009;77 Suppl 9:114-22
DeepView - Swiss-PdbViewer
3Drefine: Consistent Protein Structure Refinement by Optimizing Hydrogen Bonding Network and Atomic-Level Energy Minimization
Different energy from different programs is not a surprise. - Different principles, different approximations -
there are too many features to vary.