Re: [AMBER] Building Cyclic Peptide in xleap

From: David A Case <david.case.rutgers.edu>
Date: Thu, 21 Apr 2016 19:35:06 -0400

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


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 21 2016 - 17:00:03 PDT
Custom Search