abinitio modeling

[Anonymous]

Hi all,

I am completely new to rosetta , hope some some would help me for ab initio modeling .

rosetta.gcc aa 2ptl _ -nstruct 1 -paths ../2ptl/paths.txt > abinitio.log

here some one can explain me what is “aa” and apti_(probably fasta file)

I am not sure about paths.txt which expects to provide parameters for
pdb1, pdb2 starting strcture and status, fragment file like that

but i do not have any starting structure or any other reference structure

suggest me how to specify these parameters

If any one having sample abinitio paths.txt file please pass me.

Thank you

[Anonymous]

“aa”, “2ptl”, and “_” are “-series “, ” -protein ” and ” -chain “. Please check http://www.rosettacommons.org/tiki/tiki-index.php?page=Commands+Options+Introduction#_Query
for details.

for structure prediction, you might not need to provide start structure, but you need to provide the fragment file and the fasta (sequence) file.

> Hi all,
>
> I am completely new to rosetta , hope some some would help me for ab initio modeling .
>
> rosetta.gcc aa 2ptl _ -nstruct 1 -paths ../2ptl/paths.txt > abinitio.log
>
> here some one can explain me what is “aa” and apti_(probably fasta file)
>
> I am not sure about paths.txt which expects to provide parameters for
> pdb1, pdb2 starting strcture and status, fragment file like that
>
> but i do not have any starting structure or any other reference structure
>
> suggest me how to specify these parameters
>
> If any one having sample abinitio paths.txt file please pass me.
>
>
> Thank you
>
>

[Author]

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