How can I compute energy from a protein PDB file?
Suppose I have a protein PDB file and want to compute energy from the coordinates in the file using the following formula.
How can I do that?
Sometimes people suggest using the CONECT field for that purpose. However, some PDB files do not have this field.
Example: 4OSK.pdb (Crystal structure of TAL effector reveals the recognition between asparagine and guanine)
Related: MatterModeling.SE
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Cross-posted on bioinfo SE as well: https://bioinformatics.stackexchange.com/questions/21614/how-can-i-compute-energy-from-a-protein-pdb-file
Please mention all cross-posts.
Not at all my field of expertise, but the AMBER package is what we used in our protein bioinfo classroom exercise back in the day. I think, their force field is different, but I believe you can specify your own.
What about using pyrosetta?