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 21 2016 - 17:00:04 PDT
