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 Mon Jun 11 2012 - 17:00:02 PDT
