The problem hasn't been solved
Hi all,
I am trying to use RosettaLigand to dock a rod-shaped molecule into a protein binder with a deep, narrow binding pocket. Due to some experimental limitations, the ligand can be bound only in specific orientation - a ligand edge that is conjugated to an attached large molecule should be headed to the protein surface.
Hello,
The Rosetta program was frozen at "protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1" when I was trying to predict structure of a sequence. Dose anybody know how to solve this problem?
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I didn't find any contemporary comment on that so I'd like to ask about how to dock protein structure to dsDNA in Rosetta? Is that possible now anyhow?
I have small protein structural motif, like HTH and try to model its interaction with a sequence within dsDNA to get some hints about which residues will bind to which DNA bases so I don't have to scan along huge DNA strands but rather have a well-defined location within the major groove to explore.
Thanks for all advice.
I am using RosettaCM to build a hexon in the virus capsid. The tutorial provides membrane and non-membrane weights in the "Hybridize" step. Should I use the membrane or the non-membrane weights? Are the membrane weights applicable for any membranes?
https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial
Here is to show the stage1 weights for membrane and non-membrane
I have been trying to include an RNA as a ligand for some time now, and every attempt is a failiure. Can someone explain me how to put a whole ribonucleoprotein, RNA as ligand, into remodel? When i get a relaxed structure my interaction sites are messed up. So far i have been using constraints but i really need that RNA in there as a ligand for further research.
Hi there,
I saw most status of daemon showed [DEAD]. I had sent multiple jobs using peptiderive methods. However, till now my jobs still in queue listing. What happened actually in there? stuck?. Please response this email as soon as possible. I need these data info to make up my article. Here in my list of jobs:
I need protonation on the epsilon 2 nitrogen (HIE, HSE) and not on the (HID, HSD). The reason for this is that HID is mechanistically wrong and plays havok with my ligand.
Even though MutateResidue in pyrosetta does not accept the `mutate_self` argument it appears it calls HID HIS_D and HIE HIS and the mover thinks of them as not self of each other, so this works with switching and the heavy atoms are kept in place.
I am trying to get pymol mover to work in jupyter notebooks along with pyrosetta. I am working on windows 10 using a linux subsystem.
PyRosetta works great. I have installed pymol via anaconda3 and I have files that are a part of pymol that I can see in my terminal. When I run the following
from pyrosetta import PyMOLMover
pymol = PyMOLMover()
pymol.apply(pose)
Dear fellows,
When I generate broker.out-file with a help of minirosetta-application, I get such error:
"[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001"
although that script runs smoothly and generates a necessary file.
Could someone explain me, what means this error, please?
I will be sincerely grateful for your response and I am looking forward to it.
Best regards,
Corvin.
Hi,Is the old robetta server under maintenance now?
I want generate 3-mer and 9-mer fragment but i can not find this service in new robetta ,so i use old robetta instead.But now it seems does not work.
Does any server other than the old robetta have this function?