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Loop Modeling

Error when using next-gen KIC (Signal 6)

Category: 
Loop Modeling

Dear all,

I keep receiving a very strange error message when using NGK on a 24-core (48 mpi threads) workstation. The error occurs normally around the ~ 180 output file (once i made it to > 600 but I am aiming for at least 2000). I am trying to model up to 4 loops simultaneously but the error also appears sometimes if I model only one loop. I also tried reducing to no more than 20 threads but the error would still appear.

After googling a bit I tried to set:

ulimit -s unlimited

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how can i refine protein loop region contain nonstandard amino acid morespecifically Phosphoserine and phosphothreonine

Category: 
Loop Modeling

Recenly i have modeled one protein pknQ, its a kinase and contains phosphoserine and phoshothrionien at their activation loop region. I have used homology modeling methods to predict the 3D structure of pknQ and further refined the loop. I have modified the serine and threonine to phosphoserine and phosphothrenine now to minimize the effect of post translation modification i want to further refine loop having nonstandard amino acid (phosphorylated serine and threionine). How can i do this not getting any idea . please help

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Pre-packing a model for SWA loop building

Category: 
Loop Modeling

Dear all,

I am trying to use one of the example scripts mentioned in the paper that first described the SWA method for protein loop building [Das, R. (2013). Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. PLoS ONE 8, e74830], but it has been failing on me for reasons I do not understand.

The script is:

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Antibody protocol: unusual antibodies, and chainbreaks

Category: 
Structure prediction
Loop Modeling
ROSIE

Hello,
I am doing a research internship, on modelling some antibodies recognizing a short peptide from a conserved part of the gp41 protein of the HIV1 virus and simulating their docking.

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Error in using “loopmodel” for selective rebuilding

Category: 
Loop Modeling

Hi,

I am new to rosetta. I am trying to build the missing residue loops in 4hna sturcture. But I am getting error while generating the input file for the loopmodel application.

My input command is: loops_from_density.linuxgccrelease -database /util/rosetta/rosetta-3.2/rosetta_database/ -in:file:fullatom 4hna_9_his.pdb -edensity::mapfile apo_cut12.mrc -edensity::whole_structure_allatom_wt 1.0 -edensity::realign min -edensity::sliding_window 9 -edensity::mapreso 8.9 -edensity::grid_spacing 2.12 -max_helix_melt 1 -max_strand_melt 1 -frac_loop 0.026

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High energies after loopmodel run

Category: 
Loop Modeling

Hi everyone!

I am quite new to Rosetta and currently using the loopmodel application to remodel and refine some loops. Everything seems to be working fine. However, upon evaluation of the predicted structures I noticed the absurdly high total energies calculated for the modeled structures. When recalculated with the score_jd2 app, I get an energy of 793748.772 for the model and -1069.460 for the native structure.

Post Situation: 

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