How can I compute energy from a protein PDB file?

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13 months ago

4fzcgueyp5 • 0

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

pdb protein • 764 views

ADD COMMENT • link updated 13 months ago by yl759 ▴ 120 • written 13 months ago by 4fzcgueyp5 • 0

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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.

ADD REPLY • link 13 months ago by Ram 44k

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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.