Thanks Jason,
I will try this up
On Fri, Sep 24, 2010 at 11:25 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Sep 24 2010 - 00:00:08 PDT
