simtk.org

Hello everyone!

I have a polymer with short peptides as repeating units. In the initial minimization, the relaxation of the polymer backbone destroys the fold on some of the peptides. Is there a way to maintain the conformation of the peptides until the relaxation is over, and lift these restraints for the production run.

The only way I can think of is to restrain all the bond lengths/angles/dihedrals in the peptides explicitly. Is there a smarter/more efficient way to achieve that?


Hassan

A common way of doing this is to add harmonic restraints to the positions of some atoms, for example the backbone heavy atoms. There's sample code for doing this in the cookbook.

Restraining them in position will allow them to keep their shape but will not allow the backbone to relax. So essentially we want the peptides to rotate/translate but not lose the fold.

In that case, restraining the phi and psi dihedrals might be the best approach.