capping termini

[Firas Khatib]

Hi,

The structures that I’m generating with Rosetta are missing the hydroxyl group at the C terminus. I’m guessing this is because the residues are generated without them so that they can be connected to one another, but this is creating problems for me when I try to analyze the generated structures.

How can I run Rosetta in a way that will cap the C terminus correctly? Is there a specific option? Or a separate command? Here’s the main command in what I’m running:

“rosetta aa inpu _ -relax -farlx -termini -minimize -s highRes -fa_input -fa_output > refine.log”

When I look at files from the PDB, they have something similar to this line at the C terminus, which is the OH group:
“ATOM 2590 OXT SER B 416 48.151 19.779 122.824 1.00107.18 O”

Any help would be greatly appreciated; thanks!

Anna

[Anonymous]

Can you try to use the flag “-termini ” which invoke the modeling of both N and C termini. Or the flag “-Cterminus” which invoke the modeling of C termini residue only.

Please let me know whether this works since I never use them myself.

Yi

> Hi,
>
> The structures that I’m generating with Rosetta are missing the hydroxyl group at the C terminus. I’m guessing this is because the residues are generated without them so that they can be connected to one another, but this is creating problems for me when I try to analyze the generated structures.
>
> How can I run Rosetta in a way that will cap the C terminus correctly? Is there a specific option? Or a separate command? Here’s the main command in what I’m running:
>
> “rosetta aa inpu _ -relax -farlx -termini -minimize -s highRes -fa_input -fa_output > refine.log”
>
> When I look at files from the PDB, they have something similar to this line at the C terminus, which is the OH group:
> “ATOM 2590 OXT SER B 416 48.151 19.779 122.824 1.00107.18 O”
>
> Any help would be greatly appreciated; thanks!
>
> Anna

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