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October 25, 2011 at 7:16 am #1065Anonymous
My code creates protein models that need to be relaxed in order to lower their energy as these models may have some close contacts and other non-protein like features. According to the online documentation, the Rosetta command for relaxing non-idealized structures is
rosetta.exe aa xxx_ -relax -farlx -minimize -s xxx.start -fa_input -fa_output -use_input_bond
My questions are: 1) Is this the correct command for relaxing my models and make them “fall” in the nearest local minimum? 2) If so, how can I call these functions from inside my C++ code?
Thanks in advance,
October 25, 2011 at 1:57 pm #6178Anonymous
A) That looks suspiciously like a Rosetta++ command line, not a Rosetta3 command line. The relax documentation for 3 is here: http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_relax_command.html Which are you using, Rosetta2 (++) or Rosetta3?
Relaxation requires sampling. Running relax once from within some other code is not guaranteed to work; you have to run Relax thousands of times and take the best result.
C) Rosetta++ essentially cannot be used as a library. Rosetta3 can, but to my knowledge no one has done so yet. Start with this paper below for a description of how 3 is set up internally. To use Rosetta3 for relax as a library, you’d set up the appropriate Mover, transfer your protein structure into a Pose, and call Mover.apply(Pose). Read the paper and that will make sense.
Methods Enzymol. 2011;487:545-74.
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P.
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