You are here
The problem hasn't been solved
I was implementing the NGK loop modeling to fill the missing loops in the PDB structure, but the disulfide bonds in the PDB were broken and converted to regular cystines after the modeling. These disulfide bonds are not in the remodeled loop region and I specified '-loops:fix_natsc true'. From the output, it says:
core.conformation.Conformation: Found disulfide between residues 76 166
core.conformation.Conformation: current variant for 76 CYS
core.conformation.Conformation: current variant for 166 CYS
I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation, I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31” it shows there is no parameters for C-N-C-CA
I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsion (i.e., importing 0 1 180.00 for related parameter in mm_torsion_params.txt)
I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation , I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31” it shows there is no parameters for C-N-C-CA
I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsions (i.e., importing 0 1 180.00 for related parameter in mm_torsion_params.txt)
I would like to determine the hpatch score for proteins to predict the affinity to lignin as described by "Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity" by Sammond et al 2014 and developed hpatch by Jacak et al.
I tried to validate the method by BSA hpatch but it is not worked (the output was 8.0 whilw should be 36).
I also don't know how to obtain the hydrophobic patch area and how to identify it in protein structure.
<ROSETTASCRIPTS> <SCOREFXNS> <ScoreFunction name="r15" weights="ref2015.wts"/> </SCOREFXNS> <RESIDUE_SELECTORS> <True name="full_pose"/> </RESIDUE_SELECTORS> <TASKOPERATIONS> <ResfileCommandOperation name="rescmd" command="ALLAA EX 1 EX 2 EX_CUTOFF 1" residue_selector="full_pose"/> </TASKOPERATIONS> <MOVERS> <FastDesign name="design" scorefxn="r15" task_operations="rescmd" repeats="3">
So I've been trying to implement the new trRosetta protocol and I keep getting a segmentation fault error. Is there any idea what I might be doing incorrectly? The Rosetta Crash Log is below and is followed by the output logs (both raw text files are also included as attachments).
Has anyone had trouble with the Hybridize mover in RosettaScripts in the lastest weekly release Rosetta 2021.16 (Release date: Friday, April 23, 2021)? My script that works with older releases has stopped working and seg faults in Stage 4. Other movers, for example FastRelax, work.
Any help is much appreciated! Thanks.
I was working on a PDB structures with 3 missing loops. Two of them have more than 15 missing residues. In this case, are the loop modeling methods still applicable? If so, which algorithm should I follow? Can I ask if there is a better way to fill the loops without affecting the existing region in the PDB structure? Thank you!