Reply To: abinitio modeling

[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
>
>