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questions about ab init membrane protein

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questions about ab init membrane protein

I am trying to use the membrane ab initio modeling application by the following command: (fasta file) (span file) (path to blastpgp) (path to nr database) (path to script)

    example: (path to mini)/mini/src/apps/public/membrane_abinitio/ BRD4.fasta BRD4.span /work/bjornw/Apps/blast/bin/blastpgp /scratch/shared/genomes/nr ~bjornw/mini/src/apps/public/membrane_abinitio/

But I can't find where is (path to blastpgp) and (path to nr database), should I download these two by myself or it already includes in Rosetta3.2? could you please give me some advices for this problem?


Post Situation: 
Mon, 2011-02-07 01:09

I will try to contact the membrane ab initio folks. Those programs are not really Rosetta programs but they're part of the oldest-style fragments generating machinery. I don't think they're in the distribution but they may be in the fragments module.

Mon, 2011-02-07 09:21

Thank you very much.

Mon, 2011-02-07 10:26

Answers from a membrane_abinitio developer (in case others need them, I know you already got them albumns):

You need to download blast program (that contains blastpgp) and nr database (protein sequences database) at:

Blast program and nr database also used to generate fragments - see:

Once you install them, include full paths to their location on the command line for script.

Best regards,

Tue, 2011-02-08 11:39

I've got an error while I am running the following command:

/soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abi nitio/ test.ali test.span /usr/bin/blastp /home/albert/softbake/biosoft/rosettadb/nrdb /soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abinitio/

Error in blast output file test.ali truncated:
readline() on closed filehandle MSA at /soft/rosetta-3.2/rosetta_source/src/ap ps/public/membrane_abinitio/ line 91.

could you please tell me how to solve this?


Mon, 2011-02-14 11:43

I am also having same problem when I try to use command:

readline() on closed filehandle MSA at ./ line 91.

I wonder if I have wrong nr database. I define the correct path for nr folder. Could you please provide a solution this problem?

Wed, 2011-03-16 13:53