Scoring

Hi all,

I'm implementing a new energy term and need to weight it based on the bb h-bonding energy of this residue and the two residues it is bonded to. It is a ContextDependentOneBodyEnergy and I have everything working except this weight. Obviously rosetta already has methods that calculate hbond_lr_bb and hbond_sr_bb. My question is - what is the best way to get the hbond energys of the residues in my energy method?

Thanks!

-Igor

As each stage of AbInitio protocol call a different function (score0, score1, score2, score5 e score3), it appears to me that use a single cst_weight in my command line doesn't make sense (a single weight for every single stage). For that reason, I would like to test different weights for cst in each stage of Abinitio.

Hello,

I am a beginner in protein modelling/analysis and trying to learn through tutorials and the forums here.

A bit of a background of my present Task: I have a crystal structure of an Ab-Ag complex (AbFab with Ag peptide). I also have experimental data on binding affinities of several Ag peptide variants. I want to use this data to predict binding ability of novel Ag peptide variants with the same Ab.

Hello,

I am trying to run the domain assembly protocol while atom_pair constraints . I am using RosettaScripts for my application.

I have tried including the constraint file in the xml script using the ConstraintSetMover and Reweighting the score function. I have also tried included the constraint file in the flag file using -constraint:cst_fname. Yet the output silent do not seem to include the atom_constraints score term.

I would appreciate any help on how to include the constraints in the scoring function for domain assembly.