On Wed, 2014-03-05 at 08:02 +0000, Rasha Alqus wrote:
>
> Dear Amber usrers,
>
> I am trying to perform PMF calculation for my system using two
> restrain the distance restrain and plane -plane restrain. I have done
> minimization using these restrain and in the output file it read two
> restrains, but the energy showed that NMR restrain for bond only. I
> have also tried plane to point restrain and it showed that bond and
> plane to point in NMR restrain is used.
> I am applying the plane-plane restrain in order to prevent structure b
> to move all over structure A in z direction, when i set distance
> restrain only B structure dose not stay above A at specific distance
> (z) and location it move around A sheet in z direction.
>
> what is the problem with second restrain highlighted in red, is the
> angle set right, any other suggestion might be useful please .
Have you tried computing the restraint energy due to the plane-plane
restraint by hand to compare it to what sander is printing?
Also, I would suggest looking at the test case in
$AMBERHOME/test/plane_plane_restraint and try and change the inputs
there into your input file step at a time to determine what is different
about your input. The test properly indicates a non-zero plane-plane
restraint energy...
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 05 2014 - 05:30:04 PST
