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ValueError: can only read V2000 format files

Submitted by egecav on Wed, 2021-01-20 13:49
Category: 
PyRosetta

I'm providing the molfile_to_params.py with the enzyme-ligand complex of my molecule but unfortunetly it gives the "ValueError: can only read V2000 format files" error. Previously i gave it the individual ligand file and it processed with no problems. But when i try to process this file it doesn't seem to work. I suspect the problem is about the chemical table file formats and something in my code is from V3000 but i'm a begginer so i don't know what.

I will attach the text files of both the ligand .mol file and the complex .mol file. 

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PyRosetta - Scripts

CoupledMoves not altering backbone coordinates?

Submitted by amorin on Wed, 2021-01-20 11:38
Category: 
Design

HI All,

I'm beginning to play around with CoupledMoves for flexible backbone design and I am unable to get it to alter the protein backbone coniguration.

When I run the tutorial here (https://github.com/Kortemme-Lab/coupled_moves-tutorial) it works. But when I try and apply that (or similar) command to another protein it will deisgn the sequence, but all the output pdbs have no coordinate changes. 

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Rosetta 3 - Applications

RosettaAntibody - No matching templates for CDR1

Submitted by agctomer on Tue, 2021-01-19 22:45
Category: 
Structure prediction

hi,

I am trying to use RosettaAntibody in order to model a camiled heavy chain only antibody (pdb code: 1YC7_1).

when using the following command: 

antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta 1YC7_1.fa | tee grafting.log

(I am using exclude_homologs in order to test its preformance, because this antibody structure is already solved and found in the database).

I get the following error:

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Rosetta 3 - Applications

constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover)

Submitted by rohi on Mon, 2021-01-11 13:32
Category: 
Constraints

Hello,

I am performing Rosetta ligand docking for an enzyme A to a ligand X which should be covalently bound to a small protein B.  I need to impose this covalent bond and some other catalytic constraints (distances between ligand and receptor's residues and also the distances between two residues of the receptors )  to my ligand docking.  I  found several movers for adding constraints including AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover, but I am confused about which one works with Rosetta Ligand docking. 

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Rosetta 3 - Applications

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