On Thu, Apr 21, 2016, Maral Aminpour wrote:
>
> I am trying to make a cyclic peptide (CYS LYS LEU … MET CYS) where there
> is a disulphide bond between S of the CYS residues at both ends. This is
> how I proceed.
>
> peptide = sequence { CYX LYS LEU … MET CYX }
Note that this will have the correct covalent structure, but not the correct
3D structure--the two end cysteines will be very far apart from each other.
> 4. After edit in the xleap this is what I got (please check the figure
> attached).
?? Nothing was attached, so it's hard to know what the problem is. If you
have an initial structure with a very long S-S bond, that is what you should
expect: adding a bond term just adds that term to the force field; it does not
modify the structure into something close to a cyclic peptide.
...hope this helps...dac
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Received on Thu Apr 21 2016 - 17:00:03 PDT
