Hi Maral, hope you are well!
I am making cyclic peptides as well, my starting structure was from a
crystal structure of diphenylanyl - the attached pdb might help you move
forward with the 3D geometry so that the bonds might be closer.
~Kenneth
Kenneth N. McGuinness Ph.D
Research Associate
Advanced Science Research Center CUNY
Adviser: Dr. Rein Ulijn <http://www.ulijnlab.com/>
Cell: 928-925-7693
On Thu, Apr 21, 2016 at 7:53 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> In xleap, you can select atoms and minimize (not taking steric terms
> into account). Might be sufficient.
>
> Bill
>
> On 4/21/16 4:35 PM, David A Case wrote:
> > 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 Fri Apr 22 2016 - 10:00:03 PDT
