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Fragment files for membrane_abinitio application

Hi

I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta

The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.

Could anyone please help in this matter ?

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is it possible to ab initio only a part of a protein?

I've built a homology model but a part of it (around 12aa)is not reliable because there is no homology template in this region. The whole protein is around 350aa. And I am wondering is it possible built a ab init model based on my initial model to complete these unreliable region?

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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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