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Ab Initio

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Ab Initio

I am trying to run prediction for one of my sequence i don't have any starting structure but when i try to leave that row blank getting error message " no path"
as well as at the end of paths.txt following lines also giving error " no path for FRAGMENTS"

> 2 number of fragment files
> 3 file 1 size
> aat000_03_05.200_v1_3
> 9 file 2 size

I hope some one can provide me sample paths.txt file ab initio prediction for sequence alone.

Fri, 2008-11-21 12:42

My aim - with a peptide - is to get a PDB from a FASTA without using ROBETTA server. The latest guidelines on the web about examples for AbinitioRelax refer to "rosetta_demos/abinitio/...... ". I was unable to locate "rosetta_demos" either on the general guidelines or tutorials. What I found is a PlosOne description of combined PepFlex/Dock, which, however, starts from peptide PDB, not FASTA. Thanks for indicating where the cited rosetta_demos are located.

With so many different facets, queries to Rosetta developers are most prone to be duplications. I searched through FAQs and queries. Desolate if this is another duplication.


Wed, 2012-01-25 23:47

I believe that rosetta_demos (especially any recent Rosetta demos) are only available with the Rosetta 3 releases (particularly the most recent 3.3 release). I presume from your choice of forum, you are still using a Rosetta++/Rosetta 2 release.

At this point, the Rosetta++/Rosetta 2 releases are only recommended for replicating old results, or for those few protocols which don't yet have a Rosetta 3 version. For all new work, use of Rosetta 3 is highly recommended. Try downloading the 3.3 release, and then you should have access to the rosetta_demos directory, as well as the RosettaCON2011 Tutorials Collection (which may be a separate download).

Thu, 2012-01-26 10:42