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Structure prediction

"abinitio" with mpi

Submitted by al614 on Wed, 2016-10-12 12:17
Category: 
Structure prediction

I have looked at both documentation and this forum, and found no clear answers. I would appreciate it if someone could help.

I have compiled the mpi version to run my "ab initio" structure predictions on multiple cores.  I am not sure if I have to change my flags (such as -jran and -constant_seed etc) and my program stalls at protocols.jobdist.JobDistributors: (0) Master Node -- Waiting for job request; tag_ = 1

I use mpirun -np 4 path/to/AbinitioRelax.mpi.linuxgccrelease @flag

Thanks, any help appreciated.

-A

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Rosetta 3 - General

rosettaCM not recognizing Mn atom

Submitted by banshee on Mon, 2016-09-12 23:33
Category: 
Structure prediction

hi i am running rosettaCM with a protein which has a ligand and a heavy atome molecule, MN.

I input a params file for the ligand which rosetta sees ok, but it gives an error saying that MN is unrecognized residue.

I confirmed that MN.params file is in the right directory and the the txt file which specifies residues has the MN in it.

I also tried to input the MN.params file directly using -extra_res_fa flag but the error remains.

is metal ions not allowed when running rosettaCM? thanks.

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Rosetta 3 - Applications

Rosetta Antibody

Submitted by Maryam_tabasinezhad on Sun, 2016-08-28 00:29
Category: 
Structure prediction

Hi friends,

I want to modeling my antibody by webserver of rosetta antiboy, but I faced with the error: 

ERROR: Current DB does not cover the length of FRL of your query.
ERROR: FRL length of your query: 59
ERROR: DB: 58 or 60

Would you help me to solve the error?

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ROSIE - General

Remodel introduces clashes when stitching

Submitted by achambe on Thu, 2016-08-25 17:51
Category: 
Structure prediction

Hi all,

So I have been trying to stitch homology models together using Remodel and when it stitches the stitched piece often ends up clashing with the structure it is stitched onto. I am using the following command:

remodel.linuxgccrelease -s model3.pdb  -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -save_top 1 -overwrite -out:file:scorefile model3.sc -run:chain A >> model3.out

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Rosetta 3 - General

Question about homology modelling

Submitted by DmitriiN on Sun, 2016-08-21 13:44
Category: 
Structure prediction

Hello, everyone!

I have maybe quite a silly question.  What is the best methodic of homology modeling when my template and target have quite different lengths. Like target has 350 and the second has 260. Shall I just get rid of some tail part of longer protein during alignment? And yes, it seems that this is the best homolog for my type of protein.

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Rosetta 3 - General

Collecting all decoys from batch files

Submitted by aep on Sun, 2016-08-07 12:23
Category: 
Structure prediction

Greetings.

For anyone who's used the RASREC-based protocols in Rosetta, I'm wondering if you know of any script or straightforward way to collect the decoys generated across all batch files. I'd like to be able to plot all decoys on an energy-rms plot. I know Rosetta reuses decoy tags, so I'm not sure how to go about it. I've looked into the cluster application, but I'd like to use the centroid and/or full-atom scores for direct manual plotting as well.

Any advice would be much appreciated.

Cheers.

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Rosetta 3 - Applications

how build (N-terminal 17 residues) structre /fragment file generation

Submitted by venkatazb on Wed, 2016-07-27 23:56
Category: 
Structure prediction

Greetings, 

1) How to generate the n-terminal region say 17 residues (loop only, no homologs structure available in pblast )

2) Entire protein sequence structure got Robetta n-Terminal is only loop in MD run it’s not converging. 

Accordingly plan to do loop model is that way good way? or any other Rosetta application will help in is this situations

Kindly let me know  

Awaiting your replay

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Rosetta 3 - General

Glycan in IgG1 Fc

Submitted by seanle24245 on Fri, 2016-07-22 07:50
Category: 
Structure prediction

I'm very new to protein modeling work, but from my understanding IgG1 Fcs have a glycan between the CH2 and CH3 domains.  I downloaded an IgG1 Fc from the pdb database, but I can't seem to see where it is visually.  What does it look like and if I open up the pdb as a text file, what symbol would it be and  how would I locate it?  Also if I'm doing homology modeling with one as a template, would I have to later add in the Glycan after the model is produced?  If so how would I do that?

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PyRosetta - General

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