Dear Dr. Jason
Thanks for your reply.
Yes, I did try sleap (as another option was mentioned in AMBER archieve)
But, I got another error related to dummy atom (or a atom name):
sleap: pertab.cpp:169: static const char* mort::pertab_t::get_symbol(size_t): Assertion `element != 0' failed.
Aborted
I couldn't solve it and no archieve for this error existed.
So, any idea please
Thanks in advance
W. Flak
--- On Thu, 10/7/10, Jason Swails <jason.swails.gmail.com> wrote:
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] maximum coordination exceeded $ set pert true
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Thursday, October 7, 2010, 2:07 PM
> Did you try sleap?
>
> On Thu, Oct 7, 2010 at 9:58 AM, William Flak <williamflak.yahoo.com>
> wrote:
>
> > Dear AMBER
> > I have a problem in constructing more than 6 bonds to
> a metal ion in the
> > active site.
> > I have tried set command without any progress:
> > set complex.51.CA pert true
> > it always give me the following error:
> > Bond: maximum coordination exceeded on .R<CAX
> 51>.A<CA 1>
> > -- setting atoms pert=true
> overrides default limits
> >
> > I see, set command solved this problem for the others,
> but why it doesn't
> > work with me.
> > Is there any bugfix related to this problem?
> > Any kind of help would be appreciated
> > Thanks in advance
> > W. Flak
> >
> >
> >
> >
> >
> > _______________________________________________
> > 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
>
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Received on Thu Oct 07 2010 - 07:30:05 PDT
