Dear Modeller users,

I’ve tried to make an alpha helix from the peptide sequence (21 amino acids) using the script shown in the website (http://www.salilab.org/modeller/wiki/Make%20alpha%20helix), i.e., imposing restraints to force the alpha helical structure. I’ve tried with conjugate_gradients, molecular_dynamics and quasi_newton methods, but the output just showed a helix for a small part of the peptide, showing a coil for the rest of it. Although this is providing some information itself, and it roughly agrees with experimental data, I do want to force an alpha helical structure for the whole peptide. Do you know how this can be done? I was wondering if there is any method to grow an alpha helix just based on the backbone and once formed growing the side chains from it, thus avoiding possible highly destabilising side chain - side chain interactions precluding the helix formation.

Regards. Juan C.