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placing a constraint during structure prediction

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placing a constraint during structure prediction

I have installed rosetta 3.2.1. I want to predict the structure of a loop. The two terminal residues of the loop are cysteins. So i would like to tell the AbinitioRelax.linuxgccrelease script to consider the disulfide bond between the residues during structure prediction. Is there any option that i use with the AbinitionRelax script do achieve this ?


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Thu, 2011-04-07 08:54

Here's something from the FAQ section on CS-Rosetta's website:

"How to use known disulfide bond information in CS-ROSETTA?

In order to include the known disulfide bond information for the CS-ROSETTA structure prediction, an additional option "-in:fix_disulf disulf.cst" needs to be added to the ROSETTA3.x command line in the script, where "disulf.cst" is a disulfide bond definition file (and must be located in the same working directory unless its full path is provided as well). An example "disulf.cst" file containing a definition of two disulfide bonds (between residues Cys6 and Cys88 and between Cys38 and Cys68) is listed below:

6 88
38 68

Hope that helps.

Sat, 2011-06-11 12:52