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Docking to TM protein plus lipid bilayer

Category: 
Docking

Hi, I want to dock a protein to a TM protein embedded in a lipid bilayer.

Is there a way to do that with an implicit membrane model?

My current approach is to place explicit POPC lipids around the TM protein. 

What would be the simplest way to make Rosetta being able to read the pdb file containing POPC?

Thanks!

Post Situation: 

Misleading error message

Category: 
Structure prediction

Hi, when trying to relax a protein, I got the error message:

ERROR: unknown atom_name: 'CZH'  in residue TRP
 

However, there was no atom with the name 'CZH' in that pdb, not in TRP or any other residue.

The problem turned out to be the following block:

Post Situation: 

alignblast.pl truncated file

Category: 
Membrane

Hi all,

I'm a bit of a novice when it comes to programming with only basic training so this problem seems to be a little over my head.

        So I know this issue has been addressed before with run_lips4.pl but the resulting solutions for that seem to be either an improper name creation or a blank blast file due to incorrect blast database downloads. While my error seems to be specific to alignblast.pl.

I run run_lips4.pl with the following command:

Post Situation: 

Any backrub expert?

Category: 
Design

Dear all,

I have just started out my work in a computational protein design lab.
The first algorithm I learned at the beginning was backrub, which I know basically could be used for flexible backbone design.
After using it for a while, I have some doubt in my mind.
Would you mind sharing your valuable experience on the following situations regarding backrub?

1) I have generated 50k structures by backrub.
After removing redundant sequences, the number of unique amino acid sequence was just 1k.

Post Situation: 

Adding bridged water interaction in constraint file

Category: 
Enzyme Design

Hi,

 

I am working on Rosetta Enzyme Design Application trying to design a protein with a particular ligand in desired geometry. I wanted to define a bridged hydrogen bond interaction between the carboxylate group on the ligand and the arginine residue in protein via water molecule.

Post Situation: 

Clarify ProteinInterfaceDesign “randomness”

Category: 
Design

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro. Thanks in advance

</SCOREFXNS>

        <FILTERS>

Post Situation: 

Scons LIBPATH cannot find library

Category: 
Compilation

SCons is unable to find a shared library (libcloog-isl.so.4).

The build fails immediately with the following error:

/share/apps/NYUAD3/gcc/gcc/4.9.3/el7/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: error while loading shared libraries: libcloog-isl.so.4: cannot open shared object file: No such file or directory

I confirm that libcloog-isl.so.4 does exist:

Post Situation: 

Protein Protein Docking with bound ligands

Category: 
Docking

Hi There,

Myself Haresh, I am postdoctoral fellow at University of Toronto. I used PyRosetta for protein protein docking and working good. Usually rosetta did protein protein doking between only two proteins. Is there any avaiblity or options to do protein-protein docking with bound ligand with each protein(e.g. Protein-Ligand --- Ligand-Protein)? Thanks in advance for your help.

Looking forward to hear from you.  

Post Situation: 

Unexpected Error with RosettaCM -

Category: 
Structure prediction

Hi all,

I am hoping to get some insight, my RosettaCM is crashing for an issue I haven't seen before. See below:

Terry

Error:

 

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: stage3.wts

score_typeextract failed: fa_plane

ERROR: bad line in file stage3.wts:fa_plane 0

ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 458

BACKTRACE:

[0x5e10498]

[0x459a6ec]

[0x459aa36]

[0x459ab31]

[0x45b4083]

Post Situation: 

How to correctly incorporate constraint information into ab initio structure prediction?

Category: 
Structure prediction

Hi, I am now trying to do an ab initio structure prediction with the constraint information generated from Gremlin.

My script of ab initio structure prediction with Rosetta is as follows, with the part related to constraint data bolded:

Post Situation: 

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