You are here

Home

Structure prediction

Got error when running minirosetta.linuxgccrelease on cluster but fine on Ubuntu

Submitted by lanselibai on Mon, 2014-11-10 08:12
Category: 
Structure prediction

Dear friends,
I am trying to run minirosetta.linuxgccrelease on our cluster.

I got the following message at the end of the log file:

[ERROR] EXCN_utility_exit has been thrown from: src/core/fragment/FragmentIO.cc line: 233
ERROR: ERROR: FragmentIO: could not open file $HOME/Scratch/20141110_HC_minirosetta/input/aaC226S_HC09_05.200_v1_3

This problem seems to be Rosetta specific and not relate to the cluster. However, I do not think there is anything wrong with "aaC226S_HC09_05.200_v1_3" and it works fine on my Ubuntu.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Run PackRotamersMover on specified rotamer set

Submitted by pachecoj on Mon, 2014-11-10 06:51
Category: 
Structure prediction

Hi,

I would like to run PackRotamersMover to pack on a rotamer set which I specify. It looks like the setup code calls core::pack::pack_rotamers_setup() which builds the Dunbrack rotamer library. I'm guessing such functionality is not supported, maybe there is another mover which provides it?

Jason

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Rotamers used in fixbb

Submitted by lanselibai on Thu, 2014-11-06 02:47
Category: 
Structure prediction

Dear friends,
I am trying to use fixbb to replace some amino acid residues from a template PDB into my own sequence.

Can I ask
1) Is "-dun10" the latest rotamer database? (How can I know if it is the latest?)
2) Do I need to add additional flags (e.g. -ex1, -ex2, -ex3, -ex4) or they have been set by default?

Basically, I do not have particular requirement for the structure. So I am wondering if all the flags have been set by default?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

If "clustering.py" can be used for PDBs contain two chains?

Submitted by lanselibai on Wed, 2014-11-05 06:05
Category: 
Structure prediction

Dear friends,
Can I ask if "clustering.py" can be used for PDBs contain two chains? It works fine if there is only one chain in the PDB. However, when it comes to PDBs of two chains, it seems that no PDB structures have been processed. The following are the inputs and outputs for processing PDBs with two chains. Thank you very much.

Yours sincerely
Cheng

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Get nchi for heavy atoms

Submitted by pachecoj on Tue, 2014-11-04 19:04
Category: 
Structure prediction

Hi,

Is there a way to get the number of dihedral angles excluding the trailing hydrogen when it exists? I can manually check the residue types and subtract 1 when necessary, but I was wondering if this is already stored in a member field of Pose with an accessor function?

Thanks,
Jason

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"?

Submitted by lanselibai on Tue, 2014-11-04 14:56
Category: 
Structure prediction

Dear friends,
I would like to use "loopmodel.linuxgccrelease" to remodel an internal loop of my heavy chain (HC). It works all fine except one defect: there are some coordinates shift between the output and the input. As I will finally combine light chain (LC) structure and heavy chain (HC) structure into one PDB file, these coordinates change will make the distance between LC and HC not the same as before. Can I ask how to solve this?

The input PDB and out PDB as well as the options files are attached.

My command line is:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

"Segmentation fault" for "minirosetta.linuxgccrelease"

Submitted by lanselibai on Tue, 2014-11-04 03:17
Category: 
Structure prediction

Dear friends,
I got "Segmentation fault (core dumped)" after running "minirosetta.linuxgccrelease":

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.linuxgccrelease @/home/lanselibai/Cheng/test/LC/in/comparative_model_LC.options -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database >& /home/lanselibai/Cheng/test/LC/comparative_model_LC.log &

As suggested to test it on a debug mode (https://www.rosettacommons.org/node/3526), I have tried:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Can I assume the outputs from different runs are from a same batch?

Submitted by lanselibai on Mon, 2014-11-03 06:34
Category: 
Structure prediction

Dear friends,
I am using "minirosetta.linuxgccrelease" for homology modelling. It is recommended at least 1000 outputs are needed. However, after running 3 days, my PC got a problem and only ~500 outputs have been generated. If I run a second run, can I just run another 500 outputs and combine them together with the first batch outputs, and assume those 1000 outputs are generated from same batch?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Pages

Subscribe to RSS - Structure prediction