Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Can Fold-and-dock protocol applied to membrane proteins
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July 21, 2011 at 7:14 am #986Anonymous
Dear all,
I have a membrane protein which is a dimer. I want to fold the monomer and to assemble it to a dimer.
Can Rosetta3.2 or 3.2.1 do it?
If yes, please give some advice on option setup.Thank you!
-Justin
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July 25, 2011 at 8:41 am #5902Anonymous
No one knows the solution?
I have tried the following options:
-database /home/clzhang/rosetta3.2/rosetta_database-in:file:fasta
-in:file:frag3
-in:file:frag9
-in:file:spanfile
-in:file:lipofile
-symmetry_definition symm_def_dimer.dat
-symmetry:initialize_rigid_body_dofs-abinitio:membrane
-membrane:no_interpolate_Mpair
-membrane:Menv_penaltiesBut I got complains like: “core.scoring.SymmetricScoreFunction: Warning!!! Using a symmetric score function on a non-symmetric pose”
Does anyone knows what the problem is?
Or, currently, symmetry file cannot be recognized by membrane_denovo executable?-Justin
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May 8, 2012 at 2:46 pm #7088Anonymous
Justin, how did you get on with this? any luck?
Chris
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June 8, 2012 at 2:50 pm #7199Anonymous
The command above is completely wrong and took me down a blind alley.
My current command looks like this….
/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/minirosetta.linuxgccrelease
-run:protocol broker
-broker:setup setup_init.tpb-in:file:fasta /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock/input/eliza.FASTA
-in:file:frag3 /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock/input/aat000_03_05.200_v1_3
-in:file:frag9 /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock/input/aat000_09_05.200_v1_3
-in:file:spanfile /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock/input/eliza.span
-in:file:lipofile /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock/input/eliz.lips4
-symmetry:symmetry_definition /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock/input/elizaC4.symm
-symmetry:initialize_rigid_body_dofs
-database /home/chxcja/rosetta3.3_bundles/rosetta_database/-abinitio:membrane
-membrane:no_interpolate_Mpair -membrane:Menv_penalties -membrane:normal_cycles 100 -membrane:normal_mag 5 -membrane:center_mag 1-fold_and_dock:rigid_body_cycles 1
-fold_and_dock:rigid_body_frequency 5
-fold_and_dock:rotate_anchor_to_x
-run:reinitialize_mover_for_each_job
-score:weights score13_env_hb
-abinitio:recover_low_in_stages 0
-abinitio:rg_reweight 0.001
-abinitio:use_filters false
-packing:ex1
-packing:ex1:level 1
-packing:ex2
-packing:ex2:level 1
-packing:extrachi_cutoff 0-evaluation:symmetric_rmsd
-nstruct 20
-out:file:silent_struct_type binary
-relax:quick
-relax:jump_move-out:path:pdb /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock/pdb
-out:pdb
-out:file:silent silent.out
-no_prof_info_in_silentout
-mute core.io.database
-out:level 500
-out:file:scorefile score.scHowever I’m not sure if this is using any of the membrane settings – i get something that looks vaguely like a pore type structure but the helices are at weird angles (Ie greater than the Menv penalties should allow I think).
I’ll keep people posted on my progress but if anyone has any ideas I’d really like to hear them.
Thanks
Chris
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June 8, 2012 at 2:52 pm #7137Anonymous
EDITED NOTE: The following command is useless. Do not waste your time with it. I have left it here for the record but please don’t run this….
I run fold and dock with the following command (see below) but when I run/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/score.linuxgccrelease -database ~/rosetta3.3_bundles/rosetta_database/ -in:file:silent default-c4membrane.out -in::file::fullatom -out:output
to get a pdb file of the models the pdbs only contain 1 chain. How can I get the pdb of the complex (in this case a C4 symmetric structure).
Thanks for your help
Chris
***********************************************
/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/membrane_abinitio2.linuxgccrelease
-run:protocol broker
-broker:setup setup_init.tpb-out:file:scorefile score-membrane.sc
-in:path:database /home/chxcja/rosetta3.3_bundles/rosetta_database/-file:frag3 aat000_03_05.200_v1_3
-file:frag9 aat000_09_05.200_v1_3-symmetry:symmetry_definition elizaC4.symm
-out:file:silent default-c4membrane.out
-out:file:silent_struct_type binary
-relax:fast
-relax:jump_move
-symmetry:initialize_rigid_body_dofs-in:file:fasta eliza.FASTA
-in:file:spanfile eliza.span
-in:file:lipofile eliz.lips4-abinitio:membrane
-score:find_neighbors_3dgrid
-membrane:no_interpolate_Mpair
-membrane:Menv_penalties
-membrane:normal_cycles 1000
-membrane:normal_mag 5
-membrane:center_mag 1
-nstruct 5-fold_and_dock:rigid_body_cycles 1
-fold_and_dock:rigid_body_frequency 5
-fold_and_dock:rotate_anchor_to_x-rg_reweight 0.001
-rigid_body_cycles 1
-abinitio::recover_low_in_stages 0
-rigid_body_frequency 5
-rigid_body_disable_mc
-run:reinitialize_mover_for_each_job
> rosetta.log & -
June 14, 2012 at 7:29 pm #7255Anonymous
These are the flags that I tried to fold M2 channel, and got a GDTMM 0.70 to the native structure as a tetramer. Hope this helpful –
-run:protocol broker
-broker:setup setup_init.tpb
-database minirosetta_database
-nstruct 100
-out:file:silent_struct_type binary-in:file:fasta 2kqtA.fasta
-file:frag3 2kqtA.fasta.frags.3mers
-file:frag9 2kqtA.fasta.frags.9mers-rg_reweight 0.01
-run:reinitialize_mover_for_each_job-score:find_neighbors_3dgrid
-symmetry:symmetry_definition C4.symm
-symmetry:initialize_rigid_body_dofs
-fold_and_dock::rotate_anchor_to_x-relax:fast
-relax:jump_move-abinitio:membrane
-membrane:fixed_membrane
-membrane:no_interpolate_Mpair
-membrane:Menv_penalties-in:file:spanfile 2kqtA.span
-in:file:lipofile 2kqtA.lips4
-stage2_patch score_membrane_s2.wts_patch
-stage3a_patch score_membrane_s3a.wts_patch
-stage3b_patch score_membrane_s3b.wts_patch
-stage4_patch score_membrane_s4.wts_patch-membrane:Membed_init
-relax:membrane
-score:weights membrane_highres.wts-increase_cycles 4.3
-evaluation::gdtmm -
February 11, 2013 at 11:09 pm #8397Anonymous
Thanks Wangyr, following your suggestions it was clear that there were a few things missing from my commands.
Adding them however goves me an odd result where the actual chains are not in contact with one another.
Can anyone suggest what I might be doing wrong?
Thanks
Chris
Binary output file
http://dl.dropbox.com/u/1184313/SIT-membrane5.outCommands
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/home/chxcja/rosetta3.3_bundles/rosetta_source/bin/minirosetta.linuxgccrelease
-run:protocol broker
-broker:setup setup_init.tpb-in:file:fasta /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/eliza.FASTA
-in:file:frag3 /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/aat000_03_05.200_v1_3
-in:file:frag9 /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/aat000_09_05.200_v1_3
-in:file:spanfile /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/eliza.span
-in:file:lipofile /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/eliz.lips4
-symmetry:symmetry_definition /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock3/input/elizaC4.symm
-symmetry:initialize_rigid_body_dofs
-database /home/chxcja/rosetta3.3_bundles/rosetta_database/
-nstruct 20-abinitio:membrane
-membrane:no_interpolate_Mpair
-membrane:Menv_penalties
-membrane:normal_cycles 200
-membrane:normal_mag 5
-membrane:center_mag 1
-membrane:Membed_init
-abinitio:recover_low_in_stages 0
-abinitio:rg_reweight 0.001-fold_and_dock:rigid_body_cycles 1
-fold_and_dock:rigid_body_frequency 5
-fold_and_dock:rotate_anchor_to_x
-run:reinitialize_mover_for_each_job
-score:weights score13_env_hb-packing:ex1
-packing:ex1:level 1
-packing:ex2
-packing:ex2:level 1
-packing:extrachi_cutoff 0
-score:find_neighbors_3dgrid-evaluation:symmetric_rmsd
-relax:quick
-relax:jump_move-abinitio:stage2_patch /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/score_membrane_s2.wts_patch
-abinitio:stage3a_patch /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/score_membrane_s3a.wts_patch
-abinitio:stage3b_patch /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/score_membrane_s3b.wts_patch
-abinitio:stage4_patch /home/chxcja/rosetta3.3_bundles/SIT-membrane-fold-dock5/input/score_membrane_s4.wts_patch-out:pdb
-out:file:silent_struct_type binary
-out:file:silent SIT-membrane5.out
-no_prof_info_in_silentout
-mute core.io.database
-out:file:scorefile score.sc-relax:membrane
-score:weights membrane_highres.wts
-increase_cycles 4.3 -
February 19, 2013 at 8:47 pm #8433Anonymous
Folding membrane protein in Rosetta is always really tricky. Is this protein a channel that has charged residues in the core? If that’s the case, there are a lot parameterization need to benchmark in energy function for this kind of protein, which no one has done that yet.
Could you run a positive control to see whether this is a target protein problem or a setup problem? Using the M2 channel fasta I posted previously will be an easy and quick test.
Also, it seems like the protein you are working on is really big. Please take a look at Rhiju’s fold’n dock PNAS paper to see what’s the size limitation and how much sampling you need to have.
Best,
Ray -
June 14, 2012 at 1:35 pm #7249Anonymous
I don’t think that membrane_denovo can handle symmetry, although I don’t know for sure. The error is consistent with this hypothesis.
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February 19, 2013 at 4:57 pm #8428Anonymous
What does it do if you run it without the membrane stuff? It may be that the membrane scorefunction changes make Rosetta less likely to shove stuff together.
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