Hey, I have been trying to design a peptide for a surface receptor using the RF-diffusion, But every time I am getting a peptide that has only glycine as the residue in results. I have looked at multiple literature but could not find relevant explanation.
It's unusual for RFdiffusion, or any molecular dynamics simulation method, to yield a peptide consisting solely of glycine unless specific conditions or constraints are applied. RF diffusion is a method used to simulate the diffusion of molecules in solution, typically in the context of drug design or understanding protein-ligand interactions.
If RFdiffusion is generating a peptide consisting only of glycine, there are several potential reasons:
To address this issue, you may want to review the simulation setup, including the initial structure, force field parameters, and simulation settings. Additionally, performing multiple independent simulations or using alternative simulation methods can help validate the results and identify any discrepancies or artifacts in the simulation data.
Thank you Kais Khudhair al Hadrawi for the response. My initial inputs were not correct, I have resolved the issue.
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