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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:

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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:

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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?

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Rosetta 3 - Applications

Script for loop modeling: how to define loop sequence

Submitted by batch2k on Thu, 2014-10-30 12:58
Category: 
Loop Modeling

In the tutorial on the loop modeling, loop is defined by the fold tree in the loaded from pdb-file pose that already have residues that are "loop" and are normally missing. If I have a structure, where the loop is missing, how do I define it? As far as I understand, there's no way to do this from sequence, Do I have to make a "fake" loop structure before obtaining a possibility to really model it?

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Rosetta 3 - Applications

Abinitio Relax Error from -kill_hairpins

Submitted by attesor on Tue, 2014-10-28 05:33
Category: 
Design

I am using Rosetta 3.5 to predict protein structures using AbinitioRelax protocol.
When I specify -kill_hairpins I always got the following errors:

ERROR: [ERROR] invalid header input for kill_hairpins file.
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
Exception :

[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
ERROR: [ERROR] invalid header input for kill_hairpins file.

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Rosetta 3 - Applications

Rosetta problems: terminate called after throwing an instance of 'std::string'

Submitted by Esbenjannik on Mon, 2014-10-27 02:09
Category: 
Compilation

Hi, Im new to Rosetta and these forums, but I have a problem running Rosetta. I’ve compiled on a CentOS machine, but I keep getting segmentation faults and crashes,

e.g. I try to run AbinitioRelax.default.linuxgccrelease --help

But it crashes in the midst of output with

rmsd_dump | 2 | R| dump all pdbs for loops that
| | | are below in rmsd
terminate called after throwing an instance of 'std::string'
Abort (core dumped)

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Rosetta 3 - Build/Install

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