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Constraints

SymDock with constraints

Category: 
Docking
Constraints
Symmetry

Dear all

I been trying to perform a symmetric docking with constraints and it is not working. Reading old post residue number must be carefully set. For some reason the low-res filter is dumping all the solutions ("STRUCTURE FAILED LOW-RES FILTER"). I imagine that has to be with how I define the constraints but I even tried using AtomPair CA 52 CA 182 GAUSSIANFUNC 50.0 50.0. Please can someone have a hint of what is going on?

thanks in advance

felipet

Post Situation: 

Trouble enforcing a disulfide in loop building

Category: 
Constraints

Hello,

Like some others on this forum, I'm having some trouble getting disulfides to work. I pass

-in:fix_disulf ./disulf

where disulf is a text file containing the residue numbers of the cysteines I am trying to bridge like so:

269 280

Post Situation: 

Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

Post Situation: 

Constraints and final scoring of satisfied constraints in ab initio

Category: 
Constraints

Hello,
I have a question regarding constraints and satisfied constraints scoring.
I'm using constraint files for ab initio modeling but I can't see any attributed constraint's score in the score.sc file. Is there a special command that I need to add to obtain constrain scores for calculated structures? Which one and where should it be added (the website recommendation is not clear to me)?

Post Situation: 

A question about Multiple constraints

Category: 
Constraints

Hi, all.
I've got a question about the Multiple Constraints, is there any differences between multiple-line constraints inside and outside a MultiConstraint block?
For example, if I want to apply two constraints, CST1 and CST2, what is the difference between the following two constraint files?

file1:
MultiConstraint
CST1
CST2
END

file2: (with out MultiConstraint block)
CST1
CST2

I am not sure if they are the same.

Anyone can help me? Thanks a lot in advance.

Post Situation: 

ambiguous constraints

Category: 
Constraints

I am using ambiguous constraint file which looks as follows:

AmbiguousConstraint
AtomPair CB 5 CB 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CB 5 CG 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CB 5 CD 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CB 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CG 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CD 16 BOUNDED 2.500 5.500 0.300 NOE
END_AMBIGUOUS

Post Situation: 

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