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How to do ab initio with fixed part of protein

Submitted by eunwook on Tue, 2013-04-16 03:00

There is a amino sequence 1 to 156.

Some part of the residues which were definded by homology are between 100 and 156.

That means "I've already have a secondary structure for 100 to 156."

Finally, I want to fix between 100 and 156 residues during ab initio.

Please tell me what could I do for this work. Exactly what command do I use?

I used rosetta3.4

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Rosetta 3 - General

[TopologyBroker Exception]: BBTorsion at pos 468unitialized...unclaimed

Submitted by tevang on Wed, 2013-04-10 15:07

Greetings,

I am trying to run minirosetta to create ab initio the missing ends from a crystal structure (2JLO) as in rosetta_demos/homology_modeling_with_end_extension, but I get this strange error:

protocols.relax.FastRelax: ================== Using default script ==================
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.general_abinitio: AbrelaxMover: S_0001
loops: Extended: (-0,+0) LOOP 1 9 0 0 0
loops: Extended: (-1,+0) LOOP 467 667 0 0 0
protocols.topo_broker: Enlarged loops:

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Rosetta 3 - Applications

Give diferent chain information for a single sequence (comparative modeling)

Submitted by Martin Floor on Tue, 2013-04-02 08:59

I am trying to obtain a comparative model for a fusion protein. The query sequence have two repeats of a single motif that form a monomeric structure. The template structures are, by the way, homodimeric proteins that have this motif in two separate chains. I would like to make the model giving the relative structural information that this two chains have in the homodimer. I do not know how to said this to rosetta in the alignment file:

Query sequence:

------XXXXXXXXXXXXXXXXXXX----------XXXXXXXXXXXXXXXX--------

Template (chain A)

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Rosetta 3 - General

membrane scoring function performance

Submitted by tevang on Wed, 2013-03-20 08:40

Dear forum,

I have used the minirosetta application with the membrane_highres_t1.wts scoring function to create 1817 models. Among them only 48 had negative score, which ranged between -948.737 and -633.723. In contrast the rest of the models had score between 37700.552 and 197471.510. How can this happen? Does it mean that the scoring function is not suitable for my transmembrane protein?

Below is my parameter file:

-database /home/thomas/Programs/Rosetta3.4/rosetta_database
-run:protocol threading

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Rosetta 3 - Applications

loop re-modeling std::out_of_range

Submitted by rlwoltz on Tue, 2013-03-12 18:11

I have two problems that I couldn't solve using this forum so sorry if it's a repeat. I am trying to model the effect of a g->S mutation in an ion channel. I have already modeled the wild type protein and now I'd like to do a loop remodeling to of the alpha helix that the mutation resides in. I performed the g->s mutation using pymol mutagenesis app. I understand the script I have written is does not use all the options I should for the project but I have narrowed the error down to possibly the frag files?

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jd2 time out error

Submitted by ytao on Mon, 2013-03-04 20:47

Hi,

I'm running some modeling with symmetry docking protocol (SymDock.mpi.macosgccrelease). I noticed that some of my runs ended with an error message such as this (the exact of seconds of timeout varies):

ERROR: quick exit from job-distributor due to flag jd2::XXX and timeout of 104.5 seconds
ERROR:: Exit from: src/protocols/jd2/MPIFileBufJobDistributor.cc line: 318

This error appeared to be random that it could happen at any point of the computation and if I re-ran the computation with the same inputs and flags, the error could just go away or happen at a different point.

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