I'm trying to create a protein folding simulation where I have a pdb file with six amino acids that I know make up an alpha helix. My goal is to change the backbone angles such that it no longer represents an alpha helix and then have the algorithm find the correct conformation again.
I was hoping to find a library that allows me to specify two amino acids and an angle, and have it change the angle for me, rather than having to code the whole thing up from scratch. Does such a library exist? As of right now I'm only thinking of changing the backbone angles.
I was hoping to do this in python. I'm aware of the bio.PDB python package, but as far as I'm aware this only allows me to change individual atoms, and then I would also have to specify where I want them to be located in 3D space.
Perhaps take a look here?
C: How to "linearize" or "unfold" a PDB format structure to secondary structure?
I'd probably use the peptide placer in Chimera. You can do it via GUI or python, then you can set whatever angles you want. I think its place in 3D space is just chosen automatically at the origin of the scene but I'm not 100% sure.
See this post.
Angle Phi, Psi In Python
And look through all the posts from the right panel of this post anf yours as well. You may find a lot of helpful information.