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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Received on Tue Sep 28 2010 - 00:00:03 PDT
