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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Received on Fri Jan 29 2010 - 23:00:04 PST
