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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Received on Fri Jun 08 2012 - 10:30:03 PDT
