Hi,
I tried the same Jason. I converted the CYS to CYX in the pdb file. And
after running the tleap module it automatically forms disulfide bond in
present case. I didn't used the "bond" command in the tleap. Shall I use the
bond command in tleap or not required as the disulfide bond has already been
formed (Cystein --> Cystine).
Hirdesh
On Fri, Sep 24, 2010 at 12:01 PM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
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Received on Fri Sep 24 2010 - 04:00:04 PDT
