setup_RosettaCM.py
Submitted by browns02 on Mon, 2021-06-28 07:13
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Robetta
Submitted by Rodriguez on Fri, 2021-06-25 11:34
Category:
Fragment Generation
I want to create Robetta locally on my high-powered home computer. Does anyone have detailed instructions on how to do this?
I would appreciate any help!
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Error running D100_Docking.py
Submitted by Rodriguez on Fri, 2021-06-25 11:32
Category:
Docking
Hello,
So I am trying to run the D100_Docking.py on PyRosetta4 that I have installed on Windows 10 Bash shell. I am just trying to use the script as is before attempting my own PDB files. Below is what I did, along with the errors:
Any help is greatly appreciated!
(base) jrodriguez@DESKTOP:/mnt/c/Windows/system32$ cd /mnt/c/Users/jrodriguez/Documents/PyRosetta4
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enzyme design and scoring function
Submitted by rohi on Fri, 2021-06-25 10:29
Category:
Enzyme Design
Hello,
In enzyme design, the scoring function is enzdes.wts. Do we need to change it to the most recent scoring function (ref2015)?
Also, is SR_*_interf_E_1_2 the binding energy? can we say this score is related to specificity of an enzyme?
any suggestion is appreciated.
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Hydrogen Bonding Distances and Atom identification
Submitted by kmolloy717 on Fri, 2021-06-25 08:15
Category:
Scoring
We are using PyRosetta 2.83 to identify hydrogen bonds between atoms. For example, take the following code:
pose = pose_from_pdb("/Users/kmolloy/Downloads/2ezk.pdb")
hbond_set = pose.get_hbonds()
hbond_set.show(pose, 5)
hbond_set.show(pose,7)
This results of running this code are shown below:
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Error using ddg_monomer application (Assertion `pose.residue(resnum).name1() == wt` failed)
Submitted by sgaray on Thu, 2021-06-24 14:47
Category:
Scoring
Hi, I've unsuccessfully tried to run ddg_monomer app. I want to study the estability of a small protein after some mutations. I have used a pre-minimized pdb file as an input file, but I have the following error (last lines):
apps.public.ddg.ddg_monomer: reading in mutfile
apps.public.ddg.ddg_monomer: wt is N resnum is 25 and mut is P
apps.public.ddg.ddg_monomer: wt is Y resnum is 60 and mut is H
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How to provide multiple templates for Robetta with RosettaCM option?
Submitted by lanselibai on Wed, 2021-06-23 14:06
Category:
Structure prediction
The FAQ of robetta said "You can load multiple templates, modify the alignments, add constraints, and more before submitting.“ However, I cannot find the option for loading multiple templates on the Robetta webserver. Is that possible?
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RosettaCM: threading okay, but hybridize loses many secondary structure
Submitted by lanselibai on Wed, 2021-06-23 13:51
Category:
Structure prediction
I use two templates to run the RosettaCM, each template representing different parts of the target. The threading step can retain most of the secondary structure. However, when doing the hybridize step, one part in the target loses half of its beta-sheets. Is this a common issue?
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Problems to install rosetta rosetta_bin_linux_2021.07.61567_bundle
Submitted by rtorquato on Tue, 2021-06-22 18:05
Category:
Compilation
Hi, can some body help me.
I got this message, after use the command: ./scons.py -j22 bin mode=release extras=mpi
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RosettaCM: "Ligands must be added to all templates"
Submitted by lanselibai on Tue, 2021-06-22 10:42
Category:
Structure prediction
The RosettaCM requires Ligands must be added to all templates with a non-zero weight in the XML file!
In my case, the templates represent different parts of the target, so some template includes the ligand while some template does not. Do I really need to add the ligand to the template that does not have the ligand?
If it is necessary, how to do it? It is not likely to use some alignment to "estimate" the ligand location in the template.
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