error during docking

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zhisheng
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Joined: 2010-12-04
Category: 
Docking

Hello,

When I start running docking calculation (docking_protocol.linuxgccrelease), there was an error:

ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1290

The command I used (just for test)t is:

dock -in:file:s ./prepack_protein.pdb -in:path:database $database -docking:docking_local_refine 1 -docking:dock_pert 3 8 -docking:spin 1 -docking:dock_min 1 -docking:partners [A_B] -docking:sc_min 1 -nstruct 50 -ex1 -ex2 -out:path:pdb ./path/ -out:file:scorefile ./path/

What's the problem? Or the prepack pdb file?

cheers,

smlewis
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Joined: 2010-08-03

It probably means Rosetta doesn't like the PDB input for some reason (or doesn't like the argument to the docking_partners flag). The most common problem is zero-occupancy residues (they have coordinates, but the PDB occupancy column is zero).

Try feeding the PDB to score_jd2 (using the -out:pdb flag) to get a Rosetta-cleaned version of the PDB. You can check that it isn't missing density, or that the chains are correct (no "extra" termini around missing density), etc. Also make sure your two chains are named A and B, since that's your argument to -partners.

If that doesn't work, post your PDB here and I'll see if I can spot any obvious problems with it.

zhisheng
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Joined: 2010-12-04

Hi,

Thank you very much for help. I still failed to solve the problem. The pdf is attached. What's the problem in the file?

AttachmentSize
proteinB-C.txt 275.61 KB
smlewis
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Joined: 2010-08-03

This is a bizarre problem. I tried your command line against one of the docking "test cases" (1brs.pdb) and it works fine, so it pretty much has to be something weird with the input. I can't figure out what it is. I'll see if anyone else can.

smlewis
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Joined: 2010-08-03

I don't think is what's wrong with the PDB, given that those flags will run for a different PDB, but are you aware that the flags you're passing are mutually exclusive? docking_local_refine and dock_min will override the spin and dock_pert flags. Also, spin and dock_pert are incompatible, because one spins around to any orientation, and the other says "only vary the orientation by a little." Do you want a refinement of the input (which I doubt, given that they're many angstroms apart) or do you want search-style docking? If you take out flags until you no longer have conflicting flags it does work.

zhisheng
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Joined: 2010-12-04

Hi,

I see. Thank you very much. At the moment I generated these two subunits' structures, say A&B, independently and want to dock them together. Actually I know how these two bind with each other because the complex structure A-B, has been published. But in my case it bands to another protein (C) which I need dock to this complex A-B. What is the best or proper way to get the A-B structure and then A-B-C structure by rosetta?

cheers,

jadolfbr
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Joined: 2010-08-03

If the structure of AB is published, why not use that? If you want to use your separate chain A and chain B, align them to the crystal structure AB in pymol (Or you could trick Theseus into doing it to align by maximum-liklihood, but it would take more work). Select your chain A and chain B. Save that as a pdb file. You could then:

Miminmize/FastRelax the whole complex before docking
and/or Dock A to B using -partners A_B to refine the interface

Then - Since it looks like the docking protocol only takes a single PDB? You could load your now-ready pdb file of AB into pymol, also loading C. Save all of them as a single PDB. Check the resultant file to make sure each chain ID is unique. (I apologize if you already know this.)

Most of the time if you read the cited papers, the commands they used can be found in the supplemental. I almost always start there when trying to do something new in Rosetta...
Hope this helps a bit. If you want to do a bunch of different docking steps (do A then refine, then spin, then relax, etc.), you could try either PyRosetta or RosettaScripts....

Do you know that the interface between AB is the same in ABC? Is there any experimental data? Is C known to have contacts between both A and B? I know rosetta is only 2 body at the moment, so besides writing your own protocol, I'm not sure what else you could do...

-J

Ammu
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Joined: 2012-02-02

hi, i m new to rosetta, i have downloaded & installed rosetta3.3 software through command scons mode=release.I just want help to know how to use rosetta for protein-protein prediction, docking etc.Can anybody help me because i have to do my dissertation using rosetta...............

smlewis
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Joined: 2010-08-03

Have you ready any of the many papers published using Rosetta? That's the place to start. We can answer specific questions much better than we can answer vague ones - feel free to start new threads to ask them!

Ammu
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Joined: 2012-02-02

thanks...........ya i am reading such papers.But i am confused that is it installed correctly or not?...For installation "scons mode=release" command is correct or "scons bin mode=release" proceding with "scons bin" & "scons -h"?
can you please tell me the correct installation process................

smlewis
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Joined: 2010-08-03

"mode = release" is necessary for the speed-optimized version of the code. "bin" is necessary to build the binaries - the actual executable files - rather than just the linking libraries. The simplest command for the average user is "scons.py bin mode=release".