The way I'd go about this, if you don't know the structure of your peptide
a priori but for the fact that it is cyclical, would be to make your system
without the bond peptide.1.SG peptide.9.SG command, and instead apply a
weak bonded nmr restraint to the two sulfur atoms. Do a bit of MD, tighten
the restraint, do a bit more MD, tighten some more, until the two sulfurs
are in contact. Then extract that structure, make the PDB, and remake the
topology with the bond SG SG command in the tleap input.
Alternatively, you could just peruse random PDB structures for a
beta-hairpin or other structure with a complete backbone which puts the
first and ninth residue backbones in approximately the right orientation.
Cut out that part of the PDB file and make a new file, deleting the
existing side chains and renaming the residues to your sequence. tleap
will handle the side-chain building and then you can do the cyclization
with the same bond command.
Dave
On Fri, Apr 22, 2016 at 12:43 PM, Kenneth McGuinness <
kenneth.mcguinness.gmail.com> wrote:
> 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 - 10:00:06 PDT
