Entering edit mode
11 months ago
physicsvigna
•
0
I am using frag builder python module to generate peptide structures to compute the interaction energy for ensemble of peptides of a given sequence for a fixed bond lengths and bong angles. However, the fixed bond angles are slightly deviating from the typcial values seen in the literature. For instance, the bond angle of $C_{\alpha}--N--C$ is less than the typical value of 121 degrees and the bond angle of $C_{\alpha}--N--C$ as produced by frag builder is 111.7 degrees. Hence peptide plane is still planar. Yet the distance between the two successive $C_{\alpha}--C_{\alpha}$ is 3.721 A. Is it quite wrong to deviate by 10 degrees?
