Hi Ben,
I didn't want the people to fix the structure for me. I just didn't know
the ways to fix the structure and just wanted ideas to fix a bad structure
as in this forum, people are knowledgeable and with experience. Well I am
sorry and thanks to all who suggested.
Asma
On Tue, Jun 12, 2012 at 4:56 AM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Asma,
>
> The volunteers who contribute to this list don't have the manpower to fix
> a bad structure for you, or to investigate it in detail and tell you
> exactly what's wrong with it (which is usually about 90% of the fixing
> process anyway). As a general rule, if your problem is that the docking
> process produced a bad structure, you have two options: fix your docked
> structure, by hand if necessary, or switch to a different docking workflow.
>
> Best regards,
> Ben
>
> On 11/06/2012, at 5:24 PM, Asma Abro 28-FBAS/MSBI/F09 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
>
>
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Received on Tue Jun 12 2012 - 04:30:03 PDT
