Thanks for the comment. Just a quick question, how to checkoverlap after
energy minimisation, as that time I would only have mdcrd, output and rst
files. So how can I convert rst to inpcrd?
Thank you very much
Regards
T
On Wed, Feb 20, 2013 at 11:21 AM, case <case.biomaps.rutgers.edu> wrote:
> 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
>
>
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Received on Tue Feb 19 2013 - 22:30:02 PST
