The problem has been solved
Hi everyone,
Is there a way to add a new atom without create a new pose ?
EDIT: Maybe it is not possible, we need to edit the pdb file and reload the pose. At least, can we modify his parameters "on the fly" like vdw radius, charge, etc ... ?
I have two problems that I couldn't solve using this forum so sorry if it's a repeat. I am trying to model the effect of a g->S mutation in an ion channel. I have already modeled the wild type protein and now I'd like to do a loop remodeling to of the alpha helix that the mutation resides in. I performed the g->s mutation using pymol mutagenesis app. I understand the script I have written is does not use all the options I should for the project but I have narrowed the error down to possibly the frag files?
Hi,
I'm running some modeling with symmetry docking protocol (SymDock.mpi.macosgccrelease). I noticed that some of my runs ended with an error message such as this (the exact of seconds of timeout varies):
ERROR: quick exit from job-distributor due to flag jd2::XXX and timeout of 104.5 seconds
ERROR:: Exit from: src/protocols/jd2/MPIFileBufJobDistributor.cc line: 318
This error appeared to be random that it could happen at any point of the computation and if I re-ran the computation with the same inputs and flags, the error could just go away or happen at a different point.
Hey Guys,
We are trying to load a cleaned PDB, 2PAH into Rosetta. The Iron is in the active site, and seems to be readable and on in Rosetta.
Basically, we get this:
core.conformation.Conformation: [ WARNING ] missing heavyatom: FE on residue FE 330
core.conformation.Conformation: [ WARNING ] missing heavyatom: FE on residue FE 330
core.conformation.Conformation: [ WARNING ] missing heavyatom: FE on residue FE 330
ERROR: too many tries in fill_missing_atoms!
ERROR:: Exit from: src/core/conformation/Conformation.cc line: 2664
Hi,
I'am using a simple rosetta scripts design where I want to do three subsequent steps of mover and relax (see script at the end).
Hi guys,
Generally, I am wondering how chemically modified residues work with fragments. Specifically, is there any way to generate fragments for particular residues that have phosphorylation, carbohydrates, acetylations, etc? Second, if there is no way and one passes a fragment library for Rosetta to use, and the residues where these fragments will be built are variants such as SER_phosphorylated, what is Rosetta's behavior? Will it crash or just build the fragments as normal?
Hi everyone,
I've been attempting to create one and two-body energy tables for a rotamer set over a number of residue positions. In doing so process, I've stumbled across src/protocols/RotamerDump/RotamerDumpMover.cc, which appears to do exactly what I've been trying to achieve. The issue is that I've been unable to access this feature.
I have attempted the following:
1) using the flags "-rotamerdump:one_body -rotamerdump:two_body -rotamerdump:annealer" from any of the design methods (eg. fixbb)
I was having difficulty running run_lips.pl despite instituting the suggested changes to run_lips.pl. The result was the truncated file error from alignblast.pl that everyone mentions. The suggested changes are documented in the thread below.
http://www.rosettacommons.org/content/membrane-folding-blastpgp-error#co...