The problem hasn't been solved
Hi,
I'm using git for version control while developing some additional score terms for internal use. We are not official developers, so I can't clone the official repo, so I just downloaded the source I need (2017.08), and ran the following to get a starting point for my development:
I want to include the GDP/GTP and magnesium ions in the threading process for a tubulin homology model I am trying to make (since I do believe this is the ideal way to start formulating the homology model). For some reason, however, only the GTP is included in the output pdb. I get an error message that says:
Error: potential mismatch between sequence from alignment and sequence from PDB!
Hello,
I am interested in modeling the changes to a protein after substitution of the unnatural amino acids L-ANAP and Aladan pictured below.
It does not appear that the params for these are packaged with Rosetta. However, is there an unofficial library/repository of Rosetta params that may contain params for these amino acids?
Hi,
I have a structure. I do homology modeling of another target. The template has a peptide of length 9. The new target that I am modeling has a peptide of length 10. When I perform the modeling, the target misses that 1 residue of the peptide. Is there a way to add that residue to the end of peptide?
I tried various things:
1. Adjusting the alignement (this always messes up something) before using rosetta_cm.
Hi there,
I was trying to run this command:
Hi,
I am a new user of rosetta and tried to run tutorials with rna denovo structure prediction. However, when I ran the tutorial, the program said it could not find the rna folder and the information is kept in coarse_rna fold. So I have to create a rna fold that link to coarse_rna fold. However, in that folder, it doesn't have residue_types.txt which is hightlighted below. Could you help to solve my problem? Thank you very much.
My
Hi,
I'm trying to use the InterfaceHoles filter and get the following error:
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER holes=======================
core.scoring.packing.compute_holes_score: compute_holes_surfs try: 1
sh: 1: alpha20_surf: not found
Any idea where alpha20_surf needs to be (or if it needs to be compiled?)
Dear Rosetta Support,
I am trying to create a homology model of the tubulin protein heterodimer. I want to include the GTP/magnesium and GDP/magnesium (which are in the crystal structure template I am using) in the modelling process, but I am having problems. I keep getting an error that says either the scoring function "is not setup for nonideal/cartesian scoring", or that my residue param file, e.g. GTP.fa.tors "does not have valid atom records" (or something along those lines).
We have been working with rosetta 2016.32 for a while, which compiles just fine. recently we decided to upgrade to the 3.8 release (2017.08). compiling with 'scons mode=release' reuslts in the following error trace:
Hi,
I have been trying to dock a protein and peptide at pH 5.5 using pH_mode as described by Kilambi and Gray's protocol. However, if I omit the keep_input_protonation_state flag the SFR builder removes the protons from the protonated residues. If I keep the keep_input_protonation_state flag I get a "can not find a residue type that matches the residue HIS_P" error. Is there a fix for that?
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