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Rosetta-foldtree and docking

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Rosetta-foldtree and docking
#1

Hello everyone,

I'm using Rosetta's docking_ Protocol does the docking of two proteins (one protein is double chain and the other protein is single chain), but when I run the command:

$ROSETTA/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking

It explains that "Cannot compute center of mass of zero residues! ". How to solve this problem?

My parameter settings are as follows:

-in:file:s input_files/fgf12-1q1u.pdb
-in:file:native scn1a-7dtd_0001.pdb
-unboundrot input_files/fgf12-1q1u.pdb

-nstruct 2

-partners A_A
-dock_pert 3 8

-ex1
-ex2aro

-ignore_unrecognized_res
-ignore_zero_occupancy false

-out:path:all output_files
-out:suffix _local_dock

Run the command: $ROSETTA/main/source/bin/docking_protocol.static.linuxgccrelease @flag_local_docking

Error message:

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy input_files/fgf12-1q1u.pdb
protocols.docking.DockingProtocol: Setting docking foldtree
protocols.docking.DockingProtocol: old fold tree: FOLD_TREE  EDGE 1 138 -1  EDGE 1 139 1  EDGE 1 140 2  EDGE 1 141 3  EDGE 1 142 4

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

[ERROR] Exception caught by JobDistributor for job fgf12-1q1u_local_dock_0002

 

【The attached file is the PDB of two proteins I use】

AttachmentSize
FGF12-1q1u_0001.pdb199.26 KB
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Tue, 2022-03-15 22:49
tingting

I'm pretty sure your problem is the following: `-partners A_A`

You're using PDB chain identifiers to identify the binding partners, but you're using the same chain ID on both sides, which is confusing Rosetta because it can't figure out where to put the chains.

What you'll need to do is to rename the chains in your input PDBs such that there's one set of chain letters for one side of the interface, and another set of chain letters for the other side of the docking interface. No chain letter should be shared by the two sides of the interface. Then you can set your -partners option accordingly, such that each chain is assigned to only one side of the docking interface.

 

The other issue I see is that the PDB file you provide only has a single protein chain. If you're using that as input to the docking, then a protein-protein docking protocol isn't going to work very well, as there's only a single protein. If you want to dock two copies of the same protein (without explicitly using symmetry), you'll need to manually create a second copy of the protein, change its chain letter and then dock the two copies like you would with a heterodimer.

Wed, 2022-03-16 07:59
rmoretti

Thank you for your answer! I tried to modify the partners and PDB files, but another error occurred: 'ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 1254 fold_tree nres: 429'

What's wrong with me?

Error message:

    [ ERROR ] Error in assigning a FoldTree to a Conformation - size mismatch.

    ERROR: Conformation: fold_tree nres should match conformation nres. conformation nres: 1254 fold_tree nres: 429

Wed, 2022-03-16 21:38
tingting

It's a bit hard to say withoyut seeing the full backtrace, but it sounds like you have a pose size issue. Take a look at the number of residues, and try to match it up with your inputs. How many residues do you expect to see for the structure? How many are in each chain? Is there a way you can split things up or combine them to get 1254 residues or 429 residues? Does your input contain all the residues you expect it to?

Are you providing a native structure as an rmsd reference? If so, also check the size of your native. It should match the number of residues you have in your input structure.

Thu, 2022-03-17 08:30
rmoretti