rg cutoff

[Anonymous]

Hi,

I am beginner in using rosetta (in particular, ab initio). I tried to run rosetta for one of my sequences, but encountered an error:

structure exceeds rg cutoff: outputs a number in 20s.
REPEAT STRUCTURE 1

and the program continues … but the same error shows up in the next cycle too.

In the corresponding *.sc file it says:

no_pdbfile_fail and under rama description: rg_fail

The fragment files for the sequence were generated using robetta server.

This is the second time I am using rosetta. First time I was able to generate decoys for a different sequence. Do you have any insights on what this error is? how do I fix it?

Thank you very much,

Manu

[Anonymous]

rg means Radius of gyration. If it is too large, it means that the structure could not fold well.
To solve this problem, you can try to increase the vdw weight by add option “-vdw_reweight ” in your command line, which Reweight contribution of van der Waals score to total score by this scale factor. Default: 1.0

> Hi,
>
> I am beginner in using rosetta (in particular, ab initio). I tried to run rosetta for one of my sequences, but encountered an error:
>
> structure exceeds rg cutoff: outputs a number in 20s.
> REPEAT STRUCTURE 1
>
> and the program continues … but the same error shows up in the next cycle too.
>
> In the corresponding *.sc file it says:
>
> no_pdbfile_fail and under rama description: rg_fail
>
> The fragment files for the sequence were generated using robetta server.
>
> This is the second time I am using rosetta. First time I was able to generate decoys for a different sequence. Do you have any insights on what this error is? how do I fix it?
>
> Thank you very much,
>
> Manu

[Author]

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