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Structure prediction

Can I use next generation KIC with fragments?

Category: 
Structure prediction

Hello,

I have a question about KIC protocol. I am using the next generation protocol together with fragments. I think it should be fine but I just wanted ti double check couple of things.

Firstly, can I use fragments together with these flags? :

-loops:taboo_sampling
-loops:kic_rama2b
-loops:ramp_fa_rep
-loops:ramp_rama
-loops:kic_omega_sampling
-loops:allow_omega_move

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ERROR: Assertion Fdensity.u2 and Fdensity.u3 failed

Category: 
Structure prediction

I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to fit some strucutres to an EM density map. My script exited with the below error. Please help me troubleshoot it and let me know if you need further details. 

This is the script that's I'm running:

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blast database error

Category: 
Structure prediction

 

$ROSETTA_BIN/antibody.linuxclangrelease -fasta IGHab.fasta | tee grafting.log

 

I got following error:

 

[ERROR] EXCN_utility_exit has been thrown from: src/basic/execute.cc line: 55

ERROR: basic.execute encounter error while runnning blastp -db /short/wm35/rosetta/tools/antibody/blast_database/database.H2.20 -query grafting/h2.fasta -out grafting/h2.align -word_size 2 -outfmt 7 -max_target_seqs 1024 -evalue 2000 -matrix PAM30

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Error during running a tutorial

Category: 
Structure prediction

Hello, 

I am trying to run a tutorail (rosetta-mdff-tutorial.pdf; 3.1 Structure prediction section) but I get an error during vmd -dispdev text -e fold_rpn11_terminus.tcl or more exactly during start_rosetta_abinitio rpn11_terminus rpn11_yeast_23-306_complete [list "resid 196 to 284"] 1 [list [list "rpn11_yeast_23-306_frag9" "rpn11_yeast_23-306_frag3"]] [pwd]/input $nstruct 0 0 0. Please see its log below.

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Problems with disulphide bonds during KIC

Category: 
Structure prediction

Hello.

I am new to Rosetta. I am trying to build a model of my protein but my disulphide bond seems to break after centroid stage (I am quessing here). The disulphide thats breaking is in the loop region I am trying to model. I have googled around and found some suggestions but nothing seems to work for me. Here are my flags:

 

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Abinitio error: std::out_of_range: basic_string

Category: 
Structure prediction

I'm trying to run abinitio to predict the structure of a mutant protein homologue. using thwe following command line options:

 AbinitioRelax.macosclangrelease  -in:file:native ./input_files/input.pdb -in:file:fasta ./input_files/ACSM3.txt -in:file:frag3 ./input_files/aat000_03_05.200_v1_3 -in:file:frag9 ./input_files/aat000_09_05.200_v1_3 -database $ROSETTA3_DB -nstruct 1 -out:path ./output_files/ -out:pdb -abinitio::increase_cycles 10 -abinitio:rg_reweight 0.5 -abinitio:rsd_wt_helix 0.5 -abinitio:rsd_wt_loop 0.5

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dssp

Category: 
Structure prediction

Hello. I have a  questions about abinitio structure prediction.

How  to chang the DSSP code and let  β-bridge become L , when get a pose secondary structure. I try to change it, but I do not know how to write the code in the  dssp_state method of  StrandPairing.cc in core/scoreing/dssp directory.

Please teach me method,  if you know , thank you very much!

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How to perform abinitiorelax.mpi.linuxgccrelease in parallel mode with MPI

Category: 
Structure prediction

Hi,

I have compiled Rosetta3.8 successfully with the command " $./scons.py bin mode=release extras=mpi cxx=icc". But when I performed the command "mpirun -np 64 AbinitioRelax.mpi.linuxiccrelease @options", the error will be displayed in the end like this:

=========================================================================

===

=    BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

=     PID XXXXX RUNING AT LOCALHOST.LOCALDOMAIN

=     EXIT CODE:11

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