The problem hasn't been solved
Question on using HydrogenBondConstraintGenerator
The score function I am using is ref2015.wts. It is said that to apply constraint properly, the scorefunction being used needs to have a non-zero weight for the appropriate constraint score term. Does that mean I need to add coorndinate_constraint, atom_pair_constraint or/and angel_constraint into ref2015?
If I want to apply for constraint while docking, but want the original score (without constraint) to be displayed. Do I set mover like this?
Question on residue selector: If I have chain A and chain B. Chain A having residue 1-20 and chain B has residues 1-20. If I want to select residue 1-10 from chain A. Does the following script correct? Or I have to name residue in Chain B as 21-40 to distinguish them from residues in chain A
<RESIDUE_SELECTORS>
<Chain name="chA" chains="A"/>
<Index name="res1to10" resnums="1-10"/>
</RESIDUE_SELECTORS>
Hello,
I'm having trouble with how to generate the crystal_complex.pdb with the ligand hydrogens added. I have tried cleaning the pdb while keeping the ligand with the clean_pdb_keep_ligand.py script but the ligand in reported crystal structure has no hydrogens. Using that crystal_complex.pdb for docking study gives error: " The native pose passed to InterfaceScorecalculator does not have chain X. " Is there a way we can clean the pdb, keep ligand, and add the hydrogens?
Hi, I'm trying to group structures into clusters, but I have an error and an empty log file. A few months ago (in February / March) I didn't have a problem with it, although I did it in the same way (I think so). I have no idea where this problem comes from.
Using the AbinitioRelax protocol, I obtained a silent file with 100,000 structures (centroid representations) for a certain amino acid sequence. Now I want to group the structures into clusters and sort by energy. I use the following commands:
Hi all,
I'm new to rosetta design and looking to do ab initio folding for my first metalloprotein design. I saw the documentation (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/metalloprotein-abrelax), looked at the test inputs, and read the original paper. All of these only address His and Cys as ligands. Is there a way to do other ligands such as Glu or Asp?
Hi all,
Here is the long text of my rescent Rosetta installation process. I really appreciate if you can read it and help with the problem!
I am trying to install newest Rosetta3.12 on a cluster I am currently working with (RHEL6). The version of gcc on this cluster is gcc 4.4.7 which means I need to install a newer gcc first.
Hi All,
I came across the Coupled Moves protocol recently and it sounds like an interesting alternative to FastDesign that I've been predominantly using. I tried to implement the CoupledMoves Mover within my RosettaScripts design script, however, I keep coming across the following error:
ERROR: FoldTree:: residue_edge is undefined for root vertex
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 2317
[0m[0mprotocols.rosetta_scripts.ParsedProtocol: [0m[31m[1m[ ERROR ][0m Exception while processing procotol:
Hello,
I am trying to replicate the tutorial for RosettaCM according to the following URL:
https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM
The step 1 (using setup_RosettaCM.py) is fine where I can obtain the thread pdb file and flags and rosetta_cm.xml.
But when I tried to run step 2 (Run the Hybridize mover). It crashed.