-score_app:linmin flag not working

[Anonymous]

Hi All,

I am completely new to this forum and to rosetta, so be kind with me…

I am trying to minimize a structure using rosetta and more specifically -score_app:linmin flag together with score_jd2.linuxgccrelease. First I don’t have in my installation the score.linuxgccrelease executable, is that a mistake? Are score.linuxgccrelease and score_jd2.linuxgccrelease similar / identical /different?

Second I tried to run the following command, without much success
>score_jd2.linuxgccrelease -database $rosettadb -s 1ubiA.pdb -score_app:linmin -out:output –out:prefix linmin_
ERROR: Option matching -score_app:linmin not found in command line top-level context

Can somebody help me to find the mistake and how to correct it?

Thanks!
Fabian

[Anonymous]

The documentation is out of date (sigh…). That flag was for “score” in 3.1; score_jd2 in 3.2 did not get it ported over. You are correct that the two executeables are different, and that 3.2 does not include the older one. (You can still get 3.1 if you wanted…)

linmin is not really a good choice for minimizing a raw pdb anyway. What do you need the minimization to do?

[Anonymous]

No; I saw your other thread and emailed the responsible author for advice. You’ll hear whatever I hear.

[Anonymous]

Thanks for your answer!
Essentially I would like to learn how to perform a minimization to a comparative model, to improve it and relax it from its initial conformation (as produced by modeller for example). I was just testing on a real PDB for learning purposes. If you could tell me how is the best way to do that I will appreciate it.

Best regards,
Fabian

[Anonymous]

To truly relax a protein into Rosetta’s scorefunction, use the relax application. Minimization cannot jump over energy barriers and does not perform any searching; relaxation actually searches through conformational space.

http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_relax_command.html

Minimization finds the closest energy well; relaxation searches for a closeby deep energy well.

[Anonymous]

Thanks a lot. I have a related question, I eventually want to try rosetta for comparative modeling, but the manual page is not very clear. Are you aware of a good tutorial or course page or an example for that purpose?

Thank a lot,

Fabian

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