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Ways to improve AbRelax performance?

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Ways to improve AbRelax performance?

Dear Sir and Madam,

I would like to ask you regarding the ways to improve the performance for either FragmentPicker and AbRelax applications.

I have already done a lot of work, trying to pick the right settings and relevant to them values for both FragmentPicker and AbRelax. But, unfortunately, I haven't succeeded in generation of protein structures.

They either don't pass turned on filters, or AbRelax produces poorly folded structures without proper secondary structure.
When I turn on nonlocal setting for FragmentPicker, it is not able to produce fragment files for feasible time (calculation takes too much time, e.g. there are not still results even after 10-12 hours of work).

In addition, I ran these application through MPI or use FragmentPicker compiled under cxx11thread.

Nevertheless, these approaches haven't led me to successful outcome yet.

I would hazard to guess, that the problem lies in computational capacities of hardware. I must note that my laptop has 8 Intel i5 CPUs with 1.6 GHz performance for each one. I have read such a claim, that Rosetta is not good at modelling ab initio of protein, longer than 150 AAs. My protein consists of 264 AAs.

Would anyone be kind to tell me either the way to improve my option settings or I should just to find some more powerful hardware, please?

Best regards,


AbRelax protocol2.25 KB
FragmentPick protocol1.27 KB
Post Situation: 
Tue, 2022-04-19 06:10

Hello, Corvin,

Have you tried one of the newer DL methods (AlphaFold and RoseTTAFold) to achieve your modeling goals? ColabFold is an excellent and easy-to-use gateway to these methods.

I realize that this does not directly answer your question, but I hope it helps.


Wed, 2022-04-20 09:39

Dear nannemdp,

I am really thankful to your response.

I forgot to specify, that my protein contains a Zinc ion and I use both jump and constraints files in order to provide some additional information about Zinc-coordinated residues.

Many thanks in advance.

Kind regards,


Thu, 2022-04-21 00:50