# Docking

## Save silent results to individual directory by process ID

Category:
Docking

Hi all,

I'm running the docking_protocol application by mpirun, and I want to save silent results to individual directories determined by process ID.

I found the option "-out:path:mpi_rank_dir" may be helpful but it didn't work. How do I use this option properly?

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## Prepacking a macrocycle for docking / preserving cyclization

Category:
Docking

Dear all,

I have a macrocycle peptide obtained with simple_cycpep_predict, cycled between a Lys (Dap, Dab, and Orn too) side chain and the C-terminal carboxyl. I want to dock this peptide in a binding site with FlexPepDock. During the prepacking step, the bond between the Lys_NZ and the C atom that make the cyclization is lost and a carboxyl is restituted in the C-terminal.

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## Multiple Relax runnings

Category:
Docking

Greetings everyone,

I actually have a general question, nothing specific to a rosetta protocol. But whenever I tried running multiple calculations on a HPC that uses the same application at the same time - i.e. run 3 relax protocol for protein-protein docking, the calculations simply just stop without giving me any  ROSETTA_CRASH.log, or even going through all models. What might  be the reason? What can I do ?

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## Using specific rotamers

Category:
Docking

We're trying to run a docking study between two proteins, with the protein to be docked has a few residues with some rotamers. We want to fix these rotamers, but no matter what we try, Rosetta seems to change the rotamers between the poses. Is there a way for the rotamers to be completely fixed, so that we are docking the same version of the protein in each pose?

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## Docking HeparinSulfate to proteins using GlycanDock

Category:
Docking

Hi all,

back in the days I have use Rosetta for protein de novo prediction, but never went really deep into it.

I now wanted to use the GlycanDock application to dock an heparin molecule to a protein. However, GlycanDock does end during preparation with this error message:

ERROR: Cannot compute center of mass of zero residues!
ERROR:: Exit from: src/core/pose/util.cc line: 1408
protocols.jd2.JobDistributor: [ ERROR ]


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## Interface scores comparison

Category:
Docking

Hi all,

I performed antibody-antigen docking experiments following the Rosetta antibody-antigen docking protocols. For each antibody-antigen pair, I compared the interface scores (I_sc) among the different antigens with small difference in sequence.

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## ReplicaDock2.0 demo fails with MPIFileBufJobDistributor: (1) [ ERROR ]

Category:
Docking

Dear all,

I'm really struggeling to repeat the published procedures to run ReplicaDock2.0 (Local and Global), let alone adopt it to my needs.

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## Renumbering PDB

Category:
Docking

Hello,

I have been running this command other pdbs:

python2.7 /mnt/c/Users/No\ LOL/Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/tools/protein_tools/scripts/pdb_renumber.py \--norestart HER2_C_G3_A_full.pdb HER2_C_G3_A_full.pdb

and it has worked. Yet when I run it for my current pdb, it produces this error:

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## Ensemble Docking with RosettaDock 4.0 Protocol

Category:
Docking

Greetings,

I'm trying to perform an Ensemble Docking using RosettaDock 4.0 as the protocol. The structures were relaxed, and ensembles generated for both proteins. Once the runs start using the MPI version:

$mpirun -np 24 --hostfile$PBS_NODEFILE docking_protocol.mpi.linuxgccrelease -in:file:s ../input/4udt_AB_prepack.pdb -in:file:native ../input/4udt_xtal.pdb -unboundrot ../input/4UDT_AB_renum_noHET.pdb -nstruct 5000 -ensemble1 ensemble/4udt_A_ensemblelist -ensemble2 ensemble/4udt_B_ensemblelist -partners A_B @dock_ensemble_flags

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Category:
Docking

Hello!

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