On Wed, Feb 20, 2013, Theodosia Teo wrote:
>
> I created the input file of checkoverlap ptraj as below:
> trajin [protein]
> strip: WAT
> strip: Na+
> checkoverlap
I wouldn't strip...it's certainly possible that bad overlaps are with water or
ions.
>
> The outcome did show up with few bad overlap, but when I check with the 3D
> structure, the overlap doesn't seem like a big problem to me.
> OVERLAP: atoms 2851 (:180.HG1) and 2885 (:182.O) are too close (0.182)!
This is certainly superclose, and could lead to the VDW energies you report.
Try short careful minimizations (setting ncyc = maxcyc can be very helpful).
You may need to be patient, but 1,000 to 2,000 steps of energy minimization
ought to help a lot. Do that, then use checkoverlap again on the new
structure.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 19 2013 - 17:00:03 PST
