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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Received on Sun Jun 10 2012 - 22:30:01 PDT
