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Dear all,

Let's suppose we have the following situation:

I have an antibody structure generated by the 'antibody.linuxgccrelease' (i.e. no H3 optimization yet, just grafting)

Is it possible to score it in a similar fashion as the 'antibody_H3.linuxgccrelease' application does? I mean to score it without, H3 optimization whatsoever?

I saw that in the scoring file of a H3 optimization run we can find different terms than in a normal Talaris2014 relaxing/scoring:

I design the catalytic pocket of the enzyme and obtain new PDB.

But  when I use InterfaceAnalyzer, it occurs error.

The PDB has 3 chain , A (protein), Z(cofactor, 582) and X (ligand, 583).

How can I solve it?

I want to manually set  protonation of residues.

 I find  there are params in Rosetta database folder

 ASP_P1.params ASP_P2.params

GLU_P1.params GLU_P2.params

What are differences between ASP_P1.params and  ASP_P2.params,  and GLU_P1.params and GLU_P2.params ?

In additon,  HIS  has   two deprotonation states, HID and HIE, why there are only  one file HIS_P.params ?

The above problem pluzzes me for a long time,

Hello All,

I have a protein sequence that consists of two domains: A and B. The two domains presumably interact and there are some residue pairs that can be used as constraints. However, I don't know whether these domains interact within a single protein (A-B) or a dimer (A-B', B-A'). Given the fact that both A and B have many good templates in PDB, I thought that Rosetta comparative modeling protocol could be used to investigate these two scenarios. I would appreciate suggestions on how to set up such an analysis.

Best wishes,