Hi,
I have done the distance measurement analysis. The distance is always
greater than 3 angstrom (suggesting that there is no disulfide bond:2.05
angstrom).
Is there any way via which i can make the distance between two atoms rigid
for the starting minimization and equilibration.
Hirdesh
On Tue, Sep 28, 2010 at 12:23 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> vmd for example uses distance determination, so it can not tell you if a
> bond really is broken (pymol maybe the same). Check the SS distance and
> maybe look into the prmtop file if the bond is there or not (requires some
> number digging)
>
> Or load the amber files themselves into vmd, then it reads the bond
> information.
>
> Regards,
>
> Thomas
>
> On Tue, September 28, 2010 2:08 am, hirdesh kumar wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > -
> > _______________________________________________
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> > 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
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>
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Received on Tue Sep 28 2010 - 01:00:05 PDT
