You are here

Home

Constraints

Applying RMSD constraints using pyrosetta or Rosettascripts

Submitted by chenna on Thu, 2023-02-09 05:37
Category: 
Constraints

Hello all,

I'm interested in applying RMSD constraints to a pose using pyrosetta.

I currenly have a native pose which is deformed manually, such the the backbone RMSD with respect to the native is 1 Angstroms. 

pose.residue(r).set_xyz(a, py.rosetta.numeric.xyzVector_double_t(new_coords[0], new_coords[1], new_coords[2]))

However, when I relax (cartesian), I notice the structure relaxing back to the native, ie the RMSD decreases to ~0 Angstroms.

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

Failure to produce a cst file

Submitted by biotech on Wed, 2022-10-26 11:17
Category: 
Constraints

Hi, I generated a mincst.log using the below command:

minimize_with_cst.default.linuxgccrelease -s fe.pdb  -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /home/protein-institute/ROSETTA/rosetta_bin_linux_2020.08.61146_bundle/main/database -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false > mincst.log

then produced mincst.log file was employed for generating a cst file as input for the high-resolution protocol of ddg_monomer using the below command:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Residue outside res_map range

Submitted by to-qinbin@163.com on Sat, 2022-09-10 01:56
Category: 
Constraints

Hi, I am using Rosetta to relax a enzyme with a substrate and a cofactor. The "flags2" was from rosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs

The params file for substrate (DHD.params) and cofactor (NAP) were also used.

But errors!! How to solve this problem?

"flag2"  was scucessfull for the "1A99_1A99.pdb" inrosetta/main/demos/public/prepare_pdb_for_rosetta_with_relax/starting_inputs

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Applying dihedral constraints to TRP dipeptide minimization. ACE/NME termni.

Submitted by reoverstreet on Mon, 2022-07-11 14:39
Category: 
Constraints

I have been attempting to apply dihedral constraints to the phi/psi angles of a small TRP dipeptide minimization without success. From the output pdb it appears the second dihedral constraint is not applied to the CN atom of the Acetylayted end cap. This dihedral angle shifts to 150 degrees despite a very strong constraint. I suspect Rosetta might be selecting the first CN atom it finds which would be the methyl carbon on the NME cap rather than the carbonyl carbon on the ACE group of the same name.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Submitted by rlwoltz on Tue, 2021-08-03 23:26
Category: 
Structure prediction
Constraints
Symmetry
Membrane

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

FlexPepDock bug? Constraints do not appear in total_score?

Submitted by nrollins on Mon, 2021-07-26 14:29
Category: 
Constraints

Hi, looking for some help,

It appears that constraints do not contribute to the final score output when running the FlexPepDock ab initio protocol.

I am getting docking samples that should yield score penalties >1000 under the provided distance constraints (AtomPair FLAT_HARMONIC). However, the scorefile reports numbers consistent with the score absent of penalties (approx -550, for a protein length 300 and peptide length 5).

I provide the constraints file with the flag -constraints:cst_file

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Loop modeling with constraints

Submitted by agctomer on Sat, 2021-03-20 03:53
Category: 
Loop Modeling
Constraints

Hi,

I am trying to model a loop with a constraints file (the constraints are for the atoms of the loop).

but every time I get this message: 

[FILE]: src/core/pose/util.cc
[LINE]: 704
[START_MESSAGE]
Atom 'OVL1 31' not found

[END_MESSAGE]
[END_CRASH_REPORT]

 

I also tried to set the flag "-constraints:named" to true but it didn't help...

I am using the following command:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Issues with angle Constraints during Docking

Submitted by LeonhardJS on Thu, 2021-01-28 04:40
Category: 
Constraints

Hello,

I am setting up Docking simulations of 2 Monomers of a protein that forms monolayers at interfaces (HFBI, pdb entry 2fz6 ), so I need to constrain the possible Docking configurations to stay within the x-y plane and only beeing allowed to slightly change its orientation, due to a exposed hydrophobic patch.
I tried to use a combination of 2 angular and one Dihedral constraints. The constraint file looks like:

AngConstraint.cst:
"

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Constraints