I would like to verify the accuracy of my output.
jong3 opened this issue · 2 comments
jong3 commented
When calculating protein-protein binding energy, many parameters, such as reference_, intraR_, and interS_*, are resulting in zero. I want to know if this is normal？
tommyhuangthu commented
I checked your log file. Yes, it is normal because the zero values are only for the reference_*, intraR_*, and interS_*. And you can see the interD_* values are not always zeros.
reference_*: amino acid-specific reference energies
intraR_*: intra-Residue energy (residue internal energy)
interS_*: inter-residue energy for residues on the Same chain.
interD_*: inter-residue energy for residues on the Different chains.
The binding energy comes from the inter-residue interaction from different chains.
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Subject: [tommyhuangthu/EvoEF2] I would like to verify the accuracy of my output. (Issue #4)
When calculating protein-protein binding energy, many parameters, such as reference_, intraR_, and interS_*, are resulting in zero. I want to know if this is normal？
default.png (view on web)<https://github.com/tommyhuangthu/EvoEF2/assets/42369874/433a649c-fe2b-4aa1-b06e-a7711cbe140d>
example.pdb.txt<https://github.com/tommyhuangthu/EvoEF2/files/15397051/example.pdb.txt>
example_EvoEF2.log<https://github.com/tommyhuangthu/EvoEF2/files/15397076/example_EvoEF2.log>
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jong3 commented
Thank you for the clarification and quick response. Your explanation about the energy values was very helpful!