symmetric docking and constraints

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symmetric docking and constraints
#1

Hi,

I'm wondering if the SymDock protocols supports constraints between different subunits. For example, if I know that residue 5 in chain A is 8A away from residue 5 in chain B, can I put this into the simulation and how to do it? Giving that the SymDock protocol only sees one monomeric protein from the input.

Thanks,

Yisong

Post Situation:
Thu, 2013-05-02 12:08
ytao

Try "predicting" the residue number of the latter subunits - for example if you have a 100 residue protein and want to constrain 50 to 50, give it 50 and 150. Try with exactly one distance constraint first and check the scoring manually to make sure it came out right.

I've separately sent a query to Ingemar about how this works.

Fri, 2013-05-03 14:44
smlewis

There are currently no symmetric class of distance constraints. However, the regular constraints should work fine. As Steven suggested you would have to calculate what the residue number is for the symmetric partner. Within the program the residues are identified by 1-total number of residues of chain A + chain B. So you have to calculate what residue number residue 5 in chain B is in this numbering.

After you add the constraint (with -constraints:cst_file my.cst) make sure you get a score term in score film that says atom_pair_constraints. If not, they have not been turned on for some reason.

Tue, 2013-05-07 08:47
IAndre

ytao: Be sure to try -constraints:cst_weight (which turns on the atom_pair_constraints weight, in reference to Ingemar's second point), and also the combination (-constraints:cst_fa_weight and -constraints:cst_fa_file) if your first attempts don't work.

Ingemar: does the symmetry virtual residue affect the numbering? I think it's last, so, no?

Tue, 2013-05-07 11:40
smlewis

Hello,

I am trying to constrain a symmetric dimer but I have the following error:

..........................
protocols.symetric_docking.SymDockingLowRes: in DockingLowRes.apply
::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::
protocols.symmetric_docking.SymDockProtocol: STRUCTURE FAILED LOW-RES FILTER
protocols.symmetric_docking.SymDockProtocol: scores: -5 1.53614 5.77998
protocols.symmetric_docking.SymDockProtocol: cutoffs: 10 1 1
protocols.symmetric_docking.SymDockProtocol: REPEAT STRUCTURE 999
core.scoring.constraints.ConstraintsIO: read constraints from input/sym-const.cst
core.scoring.constraints.ConstraintsIO: Read in 1 constraints
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: initialize_rigid_body_dofs: true
protocols.symmetric_docking.SymDockProtocol: finished initial perturbation
protocols.TrialMover: Acceptance rate: 0.1
protocols.TrialMover: Acceptance rate: 0.1
protocols.TrialMover: Acceptance rate: 0.04
protocols.TrialMover: Acceptance rate: 0.02
protocols.TrialMover: Acceptance rate: 0
protocols.TrialMover: Acceptance rate: 0.02
protocols.TrialMover: Acceptance rate: 0.02
protocols.TrialMover: Acceptance rate: 0.02
protocols.TrialMover: Acceptance rate: 0.02
protocols.TrialMover: Acceptance rate: 0
protocols.symetric_docking.SymDockingLowRes: in DockingLowRes.apply
::::::::::::::::::Centroid Rigid Body Adaptive:::::::::::::::::::
protocols.symmetric_docking.SymDockProtocol: STRUCTURE FAILED LOW-RES FILTER
protocols.symmetric_docking.SymDockProtocol: scores: -4 1.19221 5.39331
protocols.symmetric_docking.SymDockProtocol: cutoffs: 10 1 1
protocols.symmetric_docking.SymDockProtocol: REPEAT STRUCTURE 1000

ERROR: Illegal attempt to score with non-identical atom set between pose and etable
ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 198
protocols.jd2.JobDistributor:

[ERROR] Exception caught by JobDistributor for job 2XSC-Shiga_INPUT_0002

[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/etable/EtableEnergy.cc line: 198
ERROR: Illegal attempt to score with non-identical atom set between pose and etable

protocols.jd2.JobDistributor: 2XSC-Shiga_INPUT_0002 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 2 jobs considered, 2 jobs attempted in 3259 seconds
protocols.jd2.JobDistributor: WARNING: The following options have been set, but have not yet been used:
-constraints:cst_fa_weight 100
-constraints:cst_weight 100
-symmetry:symmetric_rmsd
........................................

Flags I use for SymDock.default.linuxgccrelease @input/symmetric-docking-flags-dimer-const are:

-in:file:s input/INPUT.pdb
#-in:file:native input/file.pdb
-ignore_unrecognized_res
# symmetry options
-symmetry:symmetry_definition input/Shiga-dimer-00.dat # This is the location of the symmetry definition file
-symmetry:initialize_rigid_body_dofs # Initialize the rigid body positions of the subunits according to the symmetry definition file
-symmetry:symmetric_rmsd # Calculate a symmmetric rmsd. # Necessary because we have 3 chains.
# packing optinos
-packing:ex1
-packing:ex2aro
# constrains
-constraints:cst_file input/sym-const.cst
-constraints:cst_weight 100
-constraints:cst_fa_file input/sym-const.cst
-constraints:cst_fa_weight 100
# output options
-out:nstruct 2
-out:file:fullatom
-out:path:pdb /home/annalisa/DIMER/output
-out:path:score /home/annalisa/DIMER/output
-out:overwrite

CONSTRAINS
AtomPair CA 41 CA 110 HARMONIC 0.0 10.0

in which I am considering a monomer of 69 residues and I am trying to distance constrain CA 41 residue and its symmetric 110 residue of the second chain B.

Can you tell me please if there is anything wrong?

Thanks a lot,

Wed, 2014-12-03 08:35
annalisa

SymDock sets max_repeats to 1000 by default. It seems none of the 1000 trials passed the low-resolution filters (10 1 1).  You perhaps should try relaxing the low-res filters using, e.g. :

-docking:dock_lowres_filter 10 2 6  # values given based on your posted output

If the error was indeed caused by the excess of max repeat, the error message is not very informative.

Wed, 2015-10-21 13:53
attesor