I was using fragbuilder module in python to generate peptides of sizes 4, 6, and 10. However, the issue with fragbuilder module is that some of the bond angles are deviating from the standard values. For instance, C_alpha--C--N bond angle standard value is 121 degrees but fragbuilder assigns 111 degrees. This angle deviation causes a deviation in the distance between the nearest neighbor C_alpha---C_alpha and its value is 3.721 angstrom and the typical standard value is 3.8 A. Also another bond angle is a deviation from the standard value by 6 degrees which is the C_alpha---C---N whose value is 111.4 degrees and typical standard values are 117 degrees. My doubt is how much deviation is allowed for MD simulations of peptides (or proteins) while fixing the bond lengths and bonds angles ?
I think the deviation allowed for a short peptide is nothing like that for a protein as there are very few constraints on the rotation of your bonds. Steric hindrance from side chains is about the only thing to prevent rotations. Peptides rarely form helices unless in something like TFE or bound to a protein so even your 10 amino acid peptide is unlikely to form one. For MD simulations I would have thought anything should be allowed - and that would increase your chances of it binding to something else if thats what you are looking for.
In general, small deviations from the ideal bond angles and lengths are usually tolerated, as long as they are within a reasonable range. The typical acceptable deviations can be in the range of a few degrees for bond angles and a few tenths of an angstrom for bond lengths. However, it is important to note that large deviations can lead to significant structural distortions and potential artifacts in the simulation results.
If you encounter deviations in bond angles and lengths when using the fragbuilder module, you have a few options to consider:
It's worth mentioning that if you are working with peptides or proteins with non-natural residues or modifications, the standard force field parameters may not accurately capture the behavior of these systems. In such cases, specialized force fields or parameterization methods may be required to account for the unique characteristics of the system.
Susanta Roy Thanks for your reply. I am working with peptides and it is non-natural.
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