Hello Majid,
You didn't add the command I suggested in my first email. I've added the
command below:
On Mon, Aug 30, 2010 at 9:26 AM, Majid Taghdir <taghdir_amb.yahoo.com>wrote:
> Dear Jason:
>
> i am using AMBER 9 and i can not use sleap. my problem is not residue
> number. why i can not created the last bond (i can not creat more than 6
> bond to Ca) . i sent to you my protein.pdb and Ca.lib files.
>
> i am useing following commands in tleap:
>
> source leaprc.gaff
> source leaprc.ff03
> loadoff Ca2.lib
> PROT = loadpdb protein.pdb
>
set PROT.192.Ca1 pert true
> 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 a lot.
>
> Majid
>
> --- On Mon, 8/30/10, 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: Monday, August 30, 2010, 12:15 PM
>
>
> 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
> _______________________________________________
> 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 - 07:30:04 PDT
