What does your tleap script look like (every command you used)? I was
mistaken in my last email -- 192 should have been 193. Also, do you get the
same error with sleap?
--Jason
On Mon, Aug 30, 2010 at 6:43 AM, Majid Taghdir <taghdir_amb.yahoo.com>wrote:
> Dear Jason
>
> Thank you for your help but the problem was not solved. i have problem with
> creating seventh bond. i have following commands:
>
> > bond PROT.26.OD1 PROT.193.Ca
> > bond PROT.28.OD1 PROT.193.Ca
> > bond PROT.30.OD1 PROT.193.Ca
> > bond PROT.32.O PROT.193.Ca
> > bond PROT.37.OE1 PROT.193.Ca
> > bond PROT.37.OE2 PROT.193.Ca
> > bond PROT.195.O PROT.193.Ca
> Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1>
> -- setting atoms pert=true override default limits
>
> Thanks
> Majid
> --- On Sun, 8/29/10, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2
> 193>.A<Ca1>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Sunday, August 29, 2010, 2:52 PM
>
>
> 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
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 30 2010 - 05:30:04 PDT
