Hello,
You have to build the system with the disulfide bond in the first place.
Note that there are 3 different CYS residues in the amber template files:
CYS (normal, H-terminated cysteine), CYX (cystine involved in disulfide
bond), and CYM (deprotonated cysteine, no disulfide bond). If you want a
particular cystine/cysteine residue to participate in a disulfide bond, then
you must change all instances of CYS to CYX for the applicable residues in
the PDB file. Then, you have to use the 'bond" command in tleap to properly
form the bond between them. The manual will help you determine the proper
syntax.
If you use sleap, it will automatically build the disulfide bonds after you
change CYS to CYX for the desired residues.
Hope this helps,
Jason
On Fri, Sep 24, 2010 at 12:01 AM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
> Hi All,
> The crystal structure of my protein of interest consists a disulfide bond
> between two cysteine residues. But during protein preparation using tleap
> the bond was broken and corresponding hydrogen were added at the terminal
> sulfur. I run the simulation and during entire simulation the disulphide
> bond was not formed ( as obvious). I want to know how can I prevent the
> breaking of disulfide bond during md run? Shall I give the consideration to
> disulfide bond or it is ok if AMBER adds the default hydrogen atoms.
>
> Thanks,
> Hirdesh
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Sep 23 2010 - 23:00:08 PDT
