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.
Have you anyone give us some detail explanation for this issue?
In our workstation, other software such as Discovery studio could easily
recognize the disulfide bond without further modification. This is a bug or
something else?
Thanks a lot.
Jacky
2010/1/30 Jason Swails <jason.swails.gmail.com>
> Hello,
>
> On Sat, Jan 30, 2010 at 1:39 AM, jacky zhao <jackyzhao010.gmail.com>
> wrote:
> > Dear all,
> > When I using xleap to prepare my input parm, some error is happen. The
> > error message I have attached below, could you mind to help me?
> > Thank you for taking your time.
> >
> > PS:I have correct the cys to cyx in the pdb file, which is formed the
> > disuflide bond. Using xleap to view the final structure, I found that
> these
> > disulfide bond are correctly to be recognized.
> >
> >
> >
> >> saveamberparm ritu test.prmtop test.inpcrd
> > Checking Unit.
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Could not find bond parameter for: SH - SH
> > Could not find bond parameter for: SH - SH
> > Could not find bond parameter for: SH - SH
> > Could not find bond parameter for: SH - SH
> > Could not find bond parameter for: SH - SH
> > Could not find bond parameter for: SH - SH
>
> The name of the sulfur atom in CYX is SG, not SH. If you go into the
> PDB file and remove the line containing the sulfur atoms in the
> residues you changed from CYS to CYX, I believe it should work. xleap
> will add the SGs back into the structure according to the CYX template
> in the library file.
>
> Hope that helped!
> Jason
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 00:00:06 PST
