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How to design a stand-alone loop from a binding interface?

Hi, Dear colleagues!

I am new to Rosetta and am now finding whether there is a solution to my problem using powerful Resetta.

I want to cut a loop which is responsible for the binding of A to B from protein A. I need to constrain this loop so it will maintain its bound conformation though it is now in the apo form.

The problems are:
1) I need to find a way to automatically constrain it either by using disulfide bond and cyclization;
2) The loop is disulfide-bonded to the rest of the protein and this disulfide bond may be responsible for maining a turn in its bound conformation;

Post Situation: 

Rosetta Docking server

Dear Sir or Madam,

I got a problem when I was trying to submit my pdb file to Rosetta docking server. I got the message as following,

"Occupancy Error: Submitted PDB(s) have occupancy field other then '1.0'. Currently we only accept PDB's with occupancy field equal '1.0'. Please fix occupancy field and resubmit the job."

Do you know how to change occupancy field of pdb file?

Regards,

Zhanjun Hou
Karmanos Cancer Center
houz@karmanos.org

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mpi / jd2 with AbinitioRelax and relax (3.2)

Hi,

I have a working mpi compile of Rosetta 3.2, and intend to use AbinitioRelax and relax on a cluster.

Things are currently working:
- with NO EXTRA PARAMETERS in my flags file (so same flags file as for single processor). Note that I have "-run:constant_seed" and "-run:jran 1111111" in my flags file.
- using "mpirun -np 8 scriptfile" (looks like one core is used for management, and 7 used for computations, and speed improvement is ~6X versus non-mpi version)

My question relates to potential JD2 parameters I could use in my flags file.

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Domain Insertion equivalent in Rosetta 3.2

Hi,
I'm trying to get something like the domain insertion mode in 3.2. For example, I have a 100 residue protein and I'd like to remodel the 50 residues between residues 25 and 75. Should I add a jump between residues 25 and 75 and have rosetta read a movemap to fix the backbone angles of residues 1-25, and 75-100?

Thanks

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Protein design - PyRosetta Script problem

Hi,

I am running the script for protein design downloaded from http://pyrosetta.org/scripts.html.

It makes design of the last 10 aa of the protein while the rest of the protein remains unchanged.
When I calculated 100 decoys, in 99 cases I obtained the same sequence of the designed fragment (different from the native one).

When I allowed for changes of sidechains rotamers in the rest of the protein I also obtained sets of the same decoys.

It is strange... Is it ok???

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PyRosetta 2.0 Beta Strand Build

I'm having a strange issue with the beta version of PyRosetta (using 64bit Ubuntu). The phi,psi dihedral angles corresponding with an alpha-helix, when applied to a 20-mir polyA structure (this is simply from the tutorial) returns an alpha-helical structure as expected. But the dihedral angles corresponding with a beta strand (-135,140) returns a completely incorrect, wheel like structure. It's as if the changes weren't applied. Could someone confirm this with their 2.0 build?

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questions about ab init membrane protein

Hello
I am trying to use the membrane ab initio modeling application by the following command:

    run_lips.pl (fasta file) (span file) (path to blastpgp) (path to nr database) (path to alignblast.pl script)

    example: (path to mini)/mini/src/apps/public/membrane_abinitio/run_lips.pl BRD4.fasta BRD4.span /work/bjornw/Apps/blast/bin/blastpgp /scratch/shared/genomes/nr ~bjornw/mini/src/apps/public/membrane_abinitio/alignblast.pl

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Installation of rosetta 3.2 of fedore core 6 platform

Hi ,

I am trying to install rosetta 3.2 on fedore coer 6 platform but I am getting the following errors after giving scons bin mode=release command :-

[root@bmel rosetta_source]# scons bin mode=release
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/usr/local/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.

Post Situation: 

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