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Structure prediction

AbInitioRelax.mpi Hangs - Waiting for Job Request

Category: 
Structure prediction

Hi guys,

 

I recently downloaded and compiled Rosetta with MPI capabilities to take advantage of the 32 core processor we have on our workstation. Compilation went well, and I can call protocols - but they all seem to hang.

 

To help narrow things down, I am working out of the DeNovo Structure Prediction tutorial demo directory - I can call the protocol and it seems to start running as normal:

 

Post Situation: 

how to perform model quality assessment of rosetta generated models?

Category: 
Structure prediction

Dear Friends,

I am performing de novo structure prediciton fo a 382 long protein sequence. I am using Rosetta for de novo structure prediction.

Can you please let me know, what is the best method to perfornm protein model quality assessment? I have been looking at some, like MetaMQAP,QA-RecobineIt, but these servers dont work.

Also, once I get my models from programs like DMPfold, I-Tasser, and Rosetta, what should be the next approach to choose the best model among the set of models? Thanks!

Post Situation: 

Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)

Category: 
Structure prediction

Dear Friends, 

 

I am running ab initio rosetta run using openmpi:

 

mpiexec -np 16 /main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database /main/database/ @options -mpi_tracer_to_file log > log1.log &

 

I see "score.fsc" file in the folder with 2000 models, and generated a RMSD vs Energy plot, whcih gives me this (the attached plot)

Post Situation: 

How to get fragment library from robetta server for mre than 1000 residue sequence?

Category: 
Structure prediction

Dear Friends,

 

I am performing de novo structure prediction for a 1135 amino acid long sequence. I ran robetta server to generate fragments for my 1135 amino acid long sequence, but got the error : Sequence length must be between 27 and 1000 residues

Can you please et me know how to get fragments in this scenario? Thanks!

 

Post Situation: 

how to make "static" built binaries use multiple cpus like "mpi"?

Category: 
Structure prediction

Dear Friends,

 

I downloaded rosetta static binaries "Rosetta 3.10 source + binaries for Linux - as one bundle (13G)"  on my centos6.9. I can see that  the executable in the "main/source/bin" are working, but how can I run these static executables (such as "AbinitioRelax.static.linuxgccrelease" ) on multple CPUs? Can I use "mpiexec" with these executables?

 

Thanks!

Post Situation: 

Error with Formatdb of legacy blast when running "install_dependencies.pl"?

Category: 
Structure prediction

Dear Friends,

When running formatdb like this:

   

blast/bin/formatdb -o T -i nr_pfilt
    [formatdb] ERROR: Using 1000000000 bases per volume will exceed the maximum number
    of volumes formatdb can create.
    Please increase this value or do not set it at all.

I get the above error, can you please let me know how can I resolve this issue?

Thanks!

Post Situation: 

"Install_dependencies.pl" gives "Aborted" when downloading "nr" database?

Category: 
Structure prediction
Downloading nr.96.tar.gz... [OK]
Downloading nr.97.tar.gz... [OK]
Downloading nr.98.tar.gz... [OK]
Downloading nr.99.tar.gz... [OK]
Aborting....
Aborted!

Dear Friends - when running "install_dependencies.pl", I get this above error when the script downloads nr database. I ran the script thrice but it gives the same error. Could you please let me know how to solve this issue? The command line I ran is:

 

./install_dependencies.pl standard &> log.log &

 

Thanks

Post Situation: 

How to analyse multiple silent files from "Abinitiorelax" output to find best models?

Category: 
Structure prediction

Dear freinds,

 

I read more about rosetta and came up with this command line for denovo structure prediction of 382 residue long protein:

I ran it in silent mode.
 

Post Situation: 

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