On Sun, Aug 29, 2010 at 5:17 AM, Majid Taghdir <taghdir_amb.yahoo.com>wrote:
> Dear amber user :
> I am studying a protein which contains a hetroatom, calcium ion,coordinated
> within the protein through seven bonds. while I was using tleap in order to
> built these seven bonds.i can creat six bonds with no problem, but the
> seventh bond faces the following error:
>
> Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
> -- setting atoms pert=true override default limits
>
Try following these directions. Assuming Ca2 that is forming 6 bonds is
residue number 193 in your complex (which I'm going to call "complex",
though you may have named it differently), try this:
set complex.192.Ca1 pert true
Of course, substitute "complex" for whatever name you assigned your system
in leap, and substitute Ca1 for whatever name the Calcium ion has in the PDB
file you loaded (NAME, not TYPE).
Hope this helps,
Jason
P.S. One other option is trying sleap instead of tleap.
>
> I would really appreciate if some one could help me with this problem.
>
>
> Majid
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Aug 29 2010 - 08:00:03 PDT
