# Docking

## Segmentation Fault during prepacking

Category:
Docking

Dear all,

When I do prepack of a antibody-antigen complex with the following command,

mpirun -np 6 docking_prepack_protocol.mpi.linuxgccrelease\
-in:file:s nb0-ag-start.pdb\
-ex1\
-ex2\
-partners H_A\
-ensemble1 nb_ensemble.list\
-ensemble2 ag_ensemble.list\
-docking:dock_rtmin\
-out:path:all prepacking

I always get a "segmentation Fault" like the following:

[END_BACKTRACE]

Post Situation:

## RosettaAntibodyDesign: How can I run the protocol without allowing design?

Category:
Structure prediction
Docking
Design

Hi there,

I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb.

However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).

Is there any way to runn RAbD while FIXing all the CDRs?

Post Situation:

## ligand_docking ligand preparation

Category:
Docking

Can everyone tell me why my ligand FMN is twisted after using molfile_to_params.py script to prepare param file? It still looks normal when I open with pymol. But it looks twisted after I open with Maestro.

Does anyone have similar experiences?

Post Situation:

## relax and movemap

Category:
Docking

Can anyone suggest to me how to relax a protein with a non-covalent ligand? I want to make sure the ligand-binding site does not change dramatically.  In the following scenarios, which one looks reasonable:

1) relax protein with ligand; use movemap to exclude the rotamer of ligand residue

Post Situation:

## Rosetta Antibody Design: Error with foldtree: problem with the fold_tree:biggest_label != num_jump 2 1

Category:
Docking
Design

Hi all,

I'm attempting to use Rosetta Antibody Design (RAbD) v2019.35.60890 to design antibodies for a protein whose structure is a trimer.
BACKGROUND: I can successfully run the RAbD protocol on the ful trimer structure from the PDB (6VXX) with the following command:

Post Situation:

## RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?

Category:
Structure prediction
Docking

I am trying to run a basic antibody/antigen design/dock simulaton using RosettaAntibodyDesign (from Rosetta 3.12)

I am using the command:

antibody_designer.macosclangrelease \
-database /path/to/database/ \
-do_dock \
-use_epitope_constraints \
-nstruct 5 -in:file:s complex_renumbered.pdb \
-seq_design_cdrs H1 H2 H3 \
-primary_cdrs H3 \
-mintype relax \
-run_snugdock \
-run_relax \
-out:path:all ./output 

Post Situation:

## How to fold-and-dock in PyRosetta?

Category:
Structure prediction
Docking
Symmetry
PyRosetta

I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta.  I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.

How to get a foldtree with symmetry? (in my case it's just simple C3)

How to combine folding and docking?  Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)?  (It can't be that simple...)

Post Situation:

## Transmembrane helix fold-and-dock?

Category:
Structure prediction
Docking
Symmetry
Membrane

I'd like to fold-and-dock a trimeric transmembrane domain.  I mostly have the "Fold And Dock" working following the example in demos/public/symmetry_examples/fold-and-dock/.  However this is treating the transmembrane helixes as though they are in solvent (so for example any hydrophilic groups always rotate outwards).  I'd like to do something which is a combination of "Membrane Abinitio" and "Fold and Dock".  Is this possible, and how do I do it?

Post Situation:

## How to specify constraints during fold-and-dock?

Category:
Structure prediction
Docking
Constraints
Symmetry

I'm folding a protein which is a trimeric long helix bundle.  I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc).  This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves.  I'd like to constrain this to extended conformations only.

I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:

Post Situation: