Thank you very much everyone for your responses. They were really useful. It works like a charm. :)
I will just mention some details of what I have done in case in future someone else encounter the same problem.
1. My problem was that I started with an extended structure not a cyclic one so in xleap I was seeing a long bond from one S to the other end S, the bond command just takes care of the force field not the structure. Having my peptide sequence, I made the cyclic peptide using this website: http://bioware.ucd.ie/~cyclops/cgi-bin/webpep.cgi. I minimized the structure to get rid of steric terms but the bond between S-S broke with minimization.
2. Then I followed David Cerutti advice using NMR restraint to the two Sulfur atoms and I annealed the system following this tutorial: http://ambermd.org/tutorials/advanced/tutorial4/
3. Then I extracted the final structure and used "bond peptide.1.SG peptide.9.SG" and the rest MD calculations as I wanted to do before. The bond between S-S is working perfect.
Cheers!
Maral
------------------------------
Maral Aminpour, PhD
Post Doctoral Fellow
Ingenuity Lab
Department of Chemical and Materials Engineering
University of Alberta
On Apr 22, 2016, at 10:52 AM, David Cerutti <dscerutti.gmail.com> wrote:
> 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 Thu Apr 28 2016 - 08:30:04 PDT
