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
>
>
>
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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 Mon Aug 30 2010 - 08:00:06 PDT
