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Stub Libraries for DockWithHotspotMover

Submitted by ayush_patel on Sat, 2024-03-09 22:43
Category: 
Docking

Hello!

I was a little bit confused about what exactly the stub libraries are and how we are supposed to generate them. From what I understand, they're simply just disembodied residues that we consider "important" to the interface in the docked complex. So, are the stub files just generated by taking a protein structure and deleting everything except for the hotspot residue, then saving that singular residue as a PDB file? Also, is it possible to assign hotspot residues to both chains that we are docking together?

Thank you so much.

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Rosetta 3 - Applications

Deciding -nstruct for RNA FARFAR2

Submitted by mandar on Thu, 2024-03-07 22:16
Category: 
Nucleic Acids

Hi,

I want to run FARFAR2 MPI protocol to build 3D model of 70 nt long RNA with command: 

mpiexec -np 8 ${rna_denovo_mpi} -fasta seq.fasta -secstruct_file rna.secstruct -minimize_rna true -cycles 20000 -nstruct 5000 -fragment_homology_rmsd 1.2 -exclusion_match_type MATCH_YR -out:file:silent $outfile_name  > out.log

I am looking for suggestion about two parts:

1. How to decide optimal value for nstruct? I understand it could depend on RNA length, is there any thumb rule to decide -nstruct option?

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Rosetta 3 - Applications

Filters saying atom type does not exist on residue

Submitted by mdm95 on Mon, 2024-03-04 15:13
Category: 
Docking

Hi,

I'm currently try to dock a ligand into a dimeric structure using Rosettascripts. When I do normal docking everything goes okay but once I add filters it no longer functions, getting the warning  [ WARNING ] Residue 477 of type CHA does not have atom with type H4. The run will continue then fail at the end. This is the name for the atom in the PDB itself so I'm unsure what exactly is happening. I've attached the xml I'm using below, any help would be greatly appreciated! (Unfortunately the pdb was too large to attach.)

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Rosetta 3 - General

setting timeout option in MPI run

Submitted by syntekabio2019 on Mon, 2024-02-26 01:09
Category: 
Docking

Hi

I'm now trying to set timout option in my rosetta MPI run

which means that after certain period of time, whole process are automatically stopped

I run with following commands

mpirun -np 10 rosetta_scripts.mpi.linuxgccrelease @options

where options is

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Rosetta 3 - General

Global Docking with output analysis RMS

Submitted by kwu030 on Fri, 2024-02-23 09:17
Category: 
Scoring

Hello, Rosetta team

I performed global docking for two proteins and got the output.sc file, there are different "RMS"s reported, Irms, Irms_leg, cen_rms, rms, and st_rmsd, what values are more useful for analysis?  I wonder if term "rms" is calcualted based on what? since I started with two far away proteins for global docking, I wonder if this rms is calcualted based on the intinial structure?

I did not provide native structure for global docking. 

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Rosetta 3 - General

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