Did you look at the structure? As I just said, you may be able to solve
your own problem by just looking at it and see if something
is wrong.
-Dan
On Mon, Jun 11, 2012 at 2:24 PM, Asma Abro 28-FBAS/MSBI/F09 <
asma.msbi28.iiu.edu.pk> wrote:
> 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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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 - 23:30:02 PDT
