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extract docking pose from ligand docking silent file

Submitted by Ruska322 on Sat, 2019-09-07 05:21
Category: 
Docking

Hi, everyone ! I try to extract the docking pose from a silent file which contains the ligand docking results. Here is my code:

extract_pdbs.mpi.linuxgccrelease -in:file:silent job01.o  -in:file:tags BLS_0092  -extra_res_fa BLS.params -in::file::fullatom -database main/database

and the followings are output warning info:

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Rosetta 3 - Applications

ligand docking with MPI

Submitted by Ruska322 on Wed, 2019-09-04 03:47
Category: 
Docking

Hello,

I'm trying to use rosetta mpi to dock a library of molecules, but I got this error:

mpirun noticed that process rank 1 with PID 26757 on node c1117 exited on signal 6 (Aborted). It seems there is an error in one node and then causes the whole job aborted, so I wonder if there are any parameters to skip the molecules with problems and continue docking. Many thanks !

Best,

Ruska

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Rosetta 3 - Applications

Unable to create col_complex.pdb file

Submitted by sayan500 on Tue, 2019-07-30 22:08
Category: 
Docking

I am new to Rosetta and was trying Protein-Protein Docking tutorial. I was about to run a local docking but it gives me an error saying that 

"ERROR: Cannot open file "input_files/col_complex.pdb"

so when I checked the "flag_local_docking" file there is a file called col_complex.pdb needed as input. But I don't understand how to build this file.

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Rosetta 3 - General

Hydrogen bond detection and shape complementarity

Submitted by sujigeorge1979 on Fri, 2019-06-14 02:39
Category: 
Docking

HI,

I have PDB strucures of antigen- antibody complexs. want to studythe hydrogen bond pattern at the ineterface and also the shape complimentarity. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456) the command line

report_hbonds_for _plugin.linuxgccrelease

-s

-prevent packing true

sc.linuxgccrelease

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Rosetta 3 - General

Docking results

Submitted by sujigeorge1979 on Wed, 2019-06-12 23:40
Category: 
Docking

hi

I am docking an antibody to antigen using the snugdock server. Just wanted to know whtat is the reference structure in the the RMSD deviation in the score.sf files. Is it the structure with the lowest rosetta energy. In case if you want to compare the original structure of complex with decoy structure what is the easiest option. i am attaching the gnuplot out put of the Total Score Vs RMSD  . Any help would highly be appreciated

Dr. Suji george

   

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ROSIE - General

How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )

Submitted by asbelx on Sat, 2019-06-08 00:07
Category: 
Docking

Hello, I want to design my protein wit XML script as the paper  Rosetta and the Design of Ligand Binding Sites
 

I want to dock with ligand.wts(-restore_pre_talaris_2013_behavior ) 

and design protein with ref2015.wts.

But the option -restore_pre_talaris_2013_behavior seem to have impact in ref2015.wts.

How can I solve it?

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Rosetta 3 - Applications

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