Thank you for your immediately reply. You are a hard-working man that
working late into the night.
Best Wishes!
Jacky
2010/1/30 Jason Swails <jason.swails.gmail.com>
> 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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>
--
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
New Library Building 11th floor,800 Xiang Yin Road
Shanghai 200433
P.R.China
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Received on Sat Jan 30 2010 - 02:30:03 PST
