The structure is simulated without ligand, it worked fine and no such error
occured. So do you think that the problem is with the ligand? What can be
done for the rectification of the structure?
Asma
On Mon, Jun 11, 2012 at 10:20 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> As Jason said, you should visualize your structure. Checkoverlap suggested
> there are many clashes. You need to look at the system
> to figure out what the cause of these clashes are. It's possible that your
> structure is completely messed up. It's also possible that the clashes
> are minor and can be fixed with minimzation. My guess based on the extreme
> closeness is that your modeled structure is bad.
>
> -Dan
>
>
> On Mon, Jun 11, 2012 at 2:10 PM, Asma Abro 28-FBAS/MSBI/F09 <
> asma.msbi28.iiu.edu.pk> wrote:
>
> > Can anyone suggest anything with regards my problem please?
> >
> > Asma
> >
> > On Fri, Jun 8, 2012 at 10:25 PM, Asma Abro 28-FBAS/MSBI/F09 <
> > asma.msbi28.iiu.edu.pk> wrote:
> >
> > > In the structure, some atoms appear to be very close to each other.
> > >
> > > Yes it had NaN for van der Waals terms. These are the results I got
> from
> > > checkoverlap. The protein structure was modeled through homology
> > modelling
> > > and the ligand is drawn with the help of ChemDraw and both were then
> > > docked. the docked structure was minimized with Chimera and then with
> > > Ambertools prmtop and inpcrd files created, also the ligand library was
> > > made.
> > >
> > > I hope this information helps in suggestion of some fix for the
> problem.
> > >
> > > Thanks.
> > >
> > >
> > > On Fri, Jun 8, 2012 at 5:20 PM, David A Case <case.biomaps.rutgers.edu
> > >wrote:
> > >
> > >> On Fri, Jun 08, 2012, Jason Swails wrote:
> > >>
> > >> > Visualize your structure -- does it look distorted? If it does not
> > look
> > >> > distorted and it just appears that some atoms are too close,
> minimize
> > >> the
> > >> > structure (probably using more steepest decent steps than normal via
> > the
> > >> > "ncyc" input variable).
> > >>
> > >> I don't think this will help...the original post (as I remember) had
> > NaN's
> > >> for van der Waals terms. It's not clear whether the results from
> > >> checkoverlap
> > >> were complete or not. And without knowing how the structure was
> > created,
> > >> it's
> > >> not possible to know how to fix it.
> > >>
> > >> ....dac
> > >>
> > >>
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> > >>
> > >
> > >
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>
>
>
> --
> Dr. Daniel J. Sindhikara <http://goo.gl/fLAqx>
> Ritsumeikan University <http://www.ritsumei.ac.jp/eng/> - Biwako Kusatsu
> Campus <http://www.ritsumei.ac.jp/eng/html/about/abo_08.html/#kusatsu>
> sindhikara.gmail.com
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Received on Sun Jun 10 2012 - 22:30:03 PDT
