Hi Thomas,
Yes I have confirmed that the bond is broken.. I confirmed in vmd as well in
pymol (after making .pdb file from amber outputs).
Hirdesh
On Tue, Sep 28, 2010 at 11:31 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> are you sure the bond is actually broken? It just looks twisted to me. Did
> you measure the distance between S1 and S2? Note that some viewers have
> problems displaying SS-bonds if the employ a simple distance criterion to
> decide what is a bonded.
>
> Kind Regards,
>
> Thomas
>
> On Tue, September 28, 2010 1:48 am, hirdesh kumar wrote:
> > Hi All,
> > In my protein of interest, there is a disulfide bond in between two
> > residues
> > so I prepared the .pdb structure by converting *CYS to CYX* and then I
> > used
> > the* bond command* in tleap for the intact cystine formation. I generated
> > the pdb structure after tleap module preparation, there was cystine in
> the
> > structure. But Once I was done with minimization, the cystine was again
> > converted to two cysteine (disulfide bond is breakage). I want to keep
> the
> > disulphide bond intact during minimization and equilibration. I am
> > wondering
> > is there any way to keep the disulphide bond intact during minimization
> > and
> > equilibration.
> > Below mentioned is the input file for the minimization. I have also
> > attached
> > the image of the broken cystine.
> >
> >
> > Minimization with Cartesian restraints for the solute
> > &cntrl
> > imin=1, maxcyc=1000, ncyc=500,
> > ntpr=100,
> > cut =10.0,
> > ntr=1,
> > &end
> > Group input for restrained atoms
> > 100.0
> > RES 1 122
> > END
> > END
> >
> > Hirdesh
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 27 2010 - 23:30:08 PDT
