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
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Sep 27 2010 - 23:30:04 PDT
