Encouraging better packing in enzyme_design
Submitted by linucks on Thu, 2018-03-01 07:05
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Rosetta relax application for generating ensemble of structures.
Submitted by abhi_pe_acharya on Mon, 2018-02-26 09:08
How to specify a specific rotamer
Submitted by Lior_UCSF on Wed, 2018-02-21 20:35
Category:
Design
I want Rosetta to use only a specific rotamer of Histidine that I have in a pdb when designing. Is there any way to do this? I have tried using SampleRotamersFromPDB but I am unsure how to provide the pdb and I get the following error:
I include this in the command line: -packing::unboundrot his_rotamer.pdb
Error messages were:
From line 12:
Error: Element 'SampleRotamersFromPDB': This element is not expected.
7: <ScoreFunction name="score" weights="ref2015"/>
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cm_scripts
Submitted by sn on Wed, 2018-02-14 11:00
Category:
Structure prediction
Hi,
I am trying to access the cm_scripts that are used in this (http://www.pnas.org/content/109/25/9875) study. Could you please let me know where I can find these scripts?
Thank you very much.
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Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
Submitted by linucks on Tue, 2018-02-13 03:41
Category:
Scoring
Hello,
I'm running the enzyme_design application using MPI and in the scorefile that is produced, the 'description' field isn't unique across the processors, so if I run on 10 processors, I get 10 PDB files named mypdb___DE_10.pdb. Firstly, is there a way to ensure that the PDB files have unique names?
As I can't correlate the scores in the scorefile to the individual PDB file, I've renamed all my PDB files to give them unique names and am then trying to use the score_jd2 to generate a scorefile. I'm using the following flags:
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DDG_monomer application
Submitted by shadrinams on Mon, 2018-02-12 12:14
Category:
Design
Hello,
I am new in Rosetta. I would like to compare stability of the wild-type and mutated proteins using DDG_monomer. Since my protein is quite big I use the low resolution protocol for now. The results that I obtained look weird to me. Could you please tell me if they are supposed to be like this or I do something wrong?
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Icouldnot find DDMI protocol for design protein
Submitted by ladimafakher on Mon, 2018-02-12 09:22
Category:
Design
Hello
I want to design my protein by Rossetta according to DDMI protocol that is used in article"computational design of PAK1 binding protein".In this article designing of protein PAK1 done by protocol DDMI in Rossetta version 2.1. but i could not find this protocol in Rossetta 3.0. Do this protocol exist in Rossetta 3.0 with different name or this protocol removed in Rossetta3.0?the command line of this protocol according to the article mentions below:
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Denovo density didn't output a structure
Submitted by ahmadkhalifa on Mon, 2018-02-12 08:10
Category:
Structure prediction
I had a bunch of assembled fragments and I ran the below protocol on them for the fragment assignment and the genration of a consesus trajectory.
#!/bin/sh
$ROSETTA3/source/bin/denovo_density.linuxgccrelease\
-mode consensus \
-in::file::silent round1/assembled.*silent \
-consensus_frac 1.0 -energy_cut 0.05 \
-mute core
# use the old model as a starting point
cp S_0001.pdb round1_model.pdb
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Repeating sequence in Rosetta de novo protein folding
Submitted by orionshih on Wed, 2018-02-07 20:52
Category:
Structure prediction
Hi,
I am trying to do a de novo protein folding from a protein sequence with repeating Gly and Arg only.
So the sequence looks like GRGRGRGRGR..... I put the sequence onto Robetta Fragment Server and it gave me this error message:
=======================================================================================
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rosetta_mpi error
Submitted by malkeet.singh on Mon, 2018-02-05 10:29
Category:
Compilation
Hello!
I'd compiled rosetta using using extra=mpi and it was successful (no errors). moreover, I already have rosetta running without mpi options.
when i am trying to run any application (let say abinitio) it pop up an error " AbinitioRelax.mpi.linuxgccrelease: error while loading shared libraries: libcppdb.so: cannot open shared object file: No such file or directory"
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