Docking with pose_loops – frustration!

[eprocko]

Hello,
I have been having a world of trouble getting this exact scenario to work as well. Required is a .fasta file with the run name (t000.fasta) and fragment libraries (which I generated from Robetta and renamed aat000A03_05.200_v1_3 and aat000A09_05.200_v1_3). I also have a pose_loops file called t000.pose_loops containing a single line with my start and end residue defining the loop that I would like modeled. And finally there is a t000.pdb file that contains protein 1 (chain A) and protein 2 (chain separated by a TER statement.

When I run the following with the above files, I see the subsequent error:

rosetta aa t000 A -s t000.pdb -dock -pose -loop -randomize 1 -nstruct 1

“Number of residues in pdb file 420 disagrees with total_residue: 314”

So I inferred that my .pdb file containing both proteins should contain only one protein. Sure enough, when I remove the second protein and run the same command, I get:

“Docking partners are goofy….this simulation’s hosed. Did you forget a TER statement?

Any help is weclomed

[Anonymous]

Hi, we had the same problem, and we solved it adding the -use_pdbseq keyword. We believe this is connected to a numbering problem. I.e., in the pdb file for the docking the residues numbering doesn’t start from 1. Please, let me know if this solves your problem.

Real thanks for your help to our post. We were able to build libraries as you suggested, and to start some loop rebuild (though we have some other problems now). Let’s try to cooperate on this, since no help comes from the developers (sigh!).

> Hello,
> I have been having a world of trouble getting this exact scenario to work as well. Required is a .fasta file with the run name (t000.fasta) and fragment libraries (which I generated from Robetta and renamed aat000A03_05.200_v1_3 and aat000A09_05.200_v1_3). I also have a pose_loops file called t000.pose_loops containing a single line with my start and end residue defining the loop that I would like modeled. And finally there is a t000.pdb file that contains protein 1 (chain A) and protein 2 (chain separated by a TER statement.
>
> When I run the following with the above files, I see the subsequent error:
>
> rosetta aa t000 A -s t000.pdb -dock -pose -loop -randomize 1 -nstruct 1
>
> “Number of residues in pdb file 420 disagrees with total_residue: 314”
>
> So I inferred that my .pdb file containing both proteins should contain only one protein. Sure enough, when I remove the second protein and run the same command, I get:
>
> “Docking partners are goofy….this simulation’s hosed. Did you forget a TER statement?
>
> Any help is weclomed

[eprocko]

Hi there,

Thank you for the information, although I was able to get all of this to work by renumbering the second protein so that it picks up where the first lets off. This allows me to specify the two proteins for docking, and allows me to specify which loops from protein 1 and/or protein 2 that I want to flex during docking.

One thing I have learned is that in order to use -pose -loop during docking, is that one must submit a .fasta sequence containing both the protein 1 and protein 2 sequences when generating fragment libraries. This is not obvious. In addition, those sequences must be continuous (as if there were 1 sequence) and the number of residues in this “single” sequence must correspond exactly to the number of residues in the .pdb file.

It’s only taken me two weeks to figure all of this out

[Author]

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