Multiple ligands in enzyme design application
Submitted by yogeshkd on Mon, 2013-02-11 10:13
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Reading FE from 2PAH
Submitted by jadolfbr on Tue, 2013-01-29 16:10
Hey Guys,
We are trying to load a cleaned PDB, 2PAH into Rosetta. The Iron is in the active site, and seems to be readable and on in Rosetta.
Basically, we get this:
core.conformation.Conformation: [ WARNING ] missing heavyatom: FE on residue FE 330
core.conformation.Conformation: [ WARNING ] missing heavyatom: FE on residue FE 330
core.conformation.Conformation: [ WARNING ] missing heavyatom: FE on residue FE 330
ERROR: too many tries in fill_missing_atoms!
ERROR:: Exit from: src/core/conformation/Conformation.cc line: 2664
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memory issue rosetta3.4 scripts
Submitted by ast on Mon, 2013-01-28 06:25
Hi,
I'am using a simple rosetta scripts design where I want to do three subsequent steps of mover and relax (see script at the end).
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Residue variant types and fragments
Submitted by jadolfbr on Mon, 2013-01-21 09:01
Hi guys,
Generally, I am wondering how chemically modified residues work with fragments. Specifically, is there any way to generate fragments for particular residues that have phosphorylation, carbohydrates, acetylations, etc? Second, if there is no way and one passes a fragment library for Rosetta to use, and the residues where these fragments will be built are variants such as SER_phosphorylated, what is Rosetta's behavior? Will it crash or just build the fragments as normal?
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How to use RotamerDump to access one and two-body energy tables?
Submitted by msun on Wed, 2013-01-16 12:26
Hi everyone,
I've been attempting to create one and two-body energy tables for a rotamer set over a number of residue positions. In doing so process, I've stumbled across src/protocols/RotamerDump/RotamerDumpMover.cc, which appears to do exactly what I've been trying to achieve. The issue is that I've been unable to access this feature.
I have attempted the following:
1) using the flags "-rotamerdump:one_body -rotamerdump:two_body -rotamerdump:annealer" from any of the design methods (eg. fixbb)
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Membrane AbInitio
Submitted by coxford on Sat, 2012-12-22 05:06
I was having difficulty running run_lips.pl despite instituting the suggested changes to run_lips.pl. The result was the truncated file error from alignblast.pl that everyone mentions. The suggested changes are documented in the thread below.
http://www.rosettacommons.org/content/membrane-folding-blastpgp-error#co...
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favor native residue in fixBB design
Submitted by ast on Mon, 2012-12-10 06:00
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Can't find RosettaRemodel in Rosetta 3.4
Submitted by petrikigor on Mon, 2012-12-03 13:56
I have Rosetta3.4 compiled and I am trying to use RosettaRemodel as documented here, but I can't even find the executable in my rosetta_source/bin. Where is it?
Edit: solution - https://www.rosettacommons.org/content/empty-dir-rosettasourcesrcappspil...
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Beta-Peptide Design Protocol now available for academic users
Submitted by Sergey on Wed, 2012-11-28 12:32
Hi Everyone,
Our ROSIE server now have Beta-Peptide Design protocol (developed in Das Lab http://www.stanford.edu/~rhiju/ ) open for public. Please visit http://rosie.rosettacommons.org/ for documentation and job submission.
Best,
Sergey.
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fold and dock protocol not working
Submitted by ytao on Mon, 2012-11-26 15:33
Hi, Rosetta community
I'm learning to use the "fold and dock" protocol and I tried the demo(rosetta_tests/integration/tests/fold_and_dock). My output file showed a trimer configuration but the protein was not folded(pdb file attached to this post). Could anyone tell me how to fix this?
My command script is:
#!/bin/tcsh
setenv workdir /Users/ytao/Apps/rosetta/rosetta_tests/integration/tests/fold_and_dock
cd $workdir
mpiexec -np 2 $rosettaBin/minirosetta.mpi.macosgccrelease @flags -database $rosettaDB -run:constant_seed -nodelay > log
My flags are (same as the demo file):
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