Building loop extensions in a membrane protein with Remodel

[Anonymous]

Hi All,

I was wondering whether Remodel is currently compatible with the RosettaMP framework? I have a designed membrane protein and I’m trying to alter the sequence of water-exposed loops, which involves a few insertions. I’m using Remodel to do this but haven’t been able to run it using the franklin2019 scorefunction.

Here are the flags that I’m using:

-s protein.pdb

-remodel:blueprint protein_new_loops.bp

-score:weights franklin2019

-in:membrane

-ex1 -ex2

-mp:setup:spanfiles protein.span  

-ignore_unrecognized_res true

-database /mnt/storage/software/apps/Rosetta-3.12/rosetta_bin_linux_2020.08.61146_bundle/main/database

-remodel:num_trajectory 1000 -remodel:save_top 10

-out:path:all output -out:suffix $SLURM_JOBID

-out:prefix newloops_

When trying to run using these flags, I get the following error:

[FILE]: src/core/conformation/Conformation.cc

[LINE]: 725

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: Incomplete Conformation: Trying to access membrane framework data without initializing with AddMembraneMover. Exiting!

 

Any help would be greatly appreciated

 

[Anonymous]

Hi benhardy,

I got the same error when I docked membrane proteins.

ERROR: Incomplete Conformation: Trying to access membrane framework data without initializing with AddMembraneMover. Exiting!

ERROR:: Exit from: src/core/conformation/Conformation.cc line: 725

 

Here are my commands：

/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/docking_protocol.static.linuxgccrelease

-database /rosetta_bin_linux_2018.33.60351_bundle/main/database

-in:file:s protein_A_B.pdb 

-mp:setup:spanfiles protein_A_B.span 

-out:file:scorefile score.sc 

-nstruct 10

-score:weights mpframework_smooth_fa_2012.wts

 

I wonder that if this is a systematic problem or just that I did something wrong ? 

And have you solved your problem yet ?

I would be so thankful for your help.

 

 

[Anonymous]

Hi, 

It looks like you’re trying to run protein docking rather than loop building with Remodel so I can’t really give any advice as I’ve never tried that. 

You may need to include the flag “-in:membrane” to tell the docking protocol that you’re working with membrane proteins. 

Have you tried using the dedicated membrane protein-protein docking application?

https://www.rosettacommons.org/docs/latest/application_documentation/membrane_proteins/RosettaMP-App-MPDock 

 

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