Rotamer Library and Ring Puckering

[MuhammadAttaElhamouly]

Hello everyone,

I have a question about amino acids like beta-beta-dicyclohexyl-alanine, within it, there are 4 conformers as stated by P. Douglas Renfrew et al 2012 (https://doi.org/10.1371/journal.pone.0032637), with rotamer library for CA-CB, CB-CG Bonds.

The params file of this amino acid includes both the rotamer library and ring puckering.

My inquiry is, while making the rotamer library, is the application changing the ring pucker while sampling the different dihedral angles, as changing the ring conformation will defiantly favour one angle over another, resulting in different probabilities for the rotamer bins, and a chain of consequal effect of any further calculation.

I tried to make a test of making rotlib for different params, the original one with Chi angles included along with adding the ring pucker, and another params have only the Chi, the generated rotamer libraries are the same in both situations, which could say that the makerotlib application isn't including puckering of the ring while making rotlib.

[MuhammadAttaElhamouly]

Answered in #75