Hello,
On Sat, Jan 30, 2010 at 2:46 AM, jacky zhao <jackyzhao010.gmail.com> wrote:
> Thanks a lot. I have solve my problem. I found that just converting the CYS
> to CYX can fix this problem.
> As you suggestion, deleting the SG atom could pass the problem, but the
> disulfide bond could not be correctly recognized. In my simulation, this
> disulfide bond is necessary for their funcion.
> Thank you all the same:)
>
> I think the xleap could not properly recognize the formation of disulfide
> bond. So we must recorrect the pdb file to convert CYS to CYX to fix it.
CYS is the cysteine residue, that terminates with an S-H. If you wish
to make a disulfide bond, then you should change those cysteines
involved in a disulfide bond to CYX as you already did. However, to
make the disulfide bond in xleap (or tleap), you have to use the
"bond" command and specify the two Sulfur atoms you need to bond
together. (See the manual for using this command). However, if you
use sleap, the disulfide bonds will be created for you as long as the
distance between the two SG atoms is smaller than the disulfide
cutoff.
Hope this helps!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jan 30 2010 - 00:00:06 PST
