The problem hasn't been solved
Hello,
I have two questions concerning conformers in the enzyme design application:
1) Is hydrogen bonding calculated from heavy atoms only or should the conformer library contain, for example, hydroxyl groups with the hydrogen pointed in multiple directions for it to recognize when a hydrogen bond can be formed?
Hi,
I am trying to find the ddg for my mutant protein-protein complex using the resetta script in calculate_protein_protein_ddg application. I have done it with -ntruct 5 and all of them gave the same values. But I am getting the same value for both the mutant and the WT.I am not sure what's wrong.Can anyone suggest something if they have an idea?
Thanks!
I am uploading my PDB and the score file. Chain A and B represent the 2 protein in the heterodimer respectively.It also has heteroatoms at the end.
What is the best way to define a custom fold tree?
I find that -auto_setup_metals does not work for me and I'd like to set up my fold tree manually.
Thanks!
Is there a way to directly manipulate ligand dihedrals in PyRosetta? If so, which mover does this?
Thanks!
Hi,
I'd like to use new scorefunction from article by O'Meara et al., 2015, from JCTC. Acording to supplementary info the published ElecHBv2 is the Talaris2013. There is missing line 'yhh_planarity 0.5' in my installation (in comparison with published article). Should I add this line or is it set there by default? what does this line mean.
thanks,
David
Hi everyone,
I'm trying to design a peptide that binds to an enzyme. The tricky bit is that the peptide needs to be "grown" off of one end of a small molecule ligand that should dock into the active site. The ligand in question has an amide group at one of the ends, and we want to add amino acids to it. It also has a chlorine atom (pdb file attached).
What would be the best way to proceed with this problem? I'm unsure of how to let Rosetta's pepspec application know that it can add amino acids at the amide group.
Hi,
I am trying to design a higher affinity interface for my protein-protein heterodimeric complex.But I'm getting the error which says "ddg is 0.246217 failing".I'm using the script similar to minpac_optE_premin.xml in the interface_design_demo folder of rosetta_2015.05.57676.
I really need some help to make this work.
Thank you!
p.s- I'll provide any other information if you need
I seem to be having an issue with getting the binary version of the Dunbrack library to load properly in PyRosetta on Windows and I was wondering if anyone knows if there is a fix for it. Obviously it takes about 30 seconds or so to load the Dunbrack libraries from text so it can turn into a rate-limiting step if you have to read these files a lot.
I installed the latest rosetta common (rosetta_src_2015.05.57576_bundle.tgz) and tried the following demo with error:
/demos/protocol_capture/2012/ligand_water_docking
setting ligand_soft_rep weight hack_elec to 0.42
ERROR: unrecognized score_type type hack_elec
ERROR:: Exit from: src/core/scoring/ScoreTypeManager.cc line: 477
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job '1HXW_input_0001'
Error:
Hi,
Bit confused on centroid scoring, which score function is recommended now, is it score3, score4, cen_std or have they been superceeded now like the talaris13 score for full atom?
Thx
Mark