On Wed, May 08, 2013 at 10:16:20AM +0200, Karl N. Kirschner wrote:
> Hello Reinis,
Thanks for reply!
>
> Have you checked to see if the difference in atom sequence
> ordering for an improper have an effect on the resulting
> modeling of the improper? In other words, does it effect the
> out-of-plane bending energies?
I have not checked this, but the equilibrium structure and
dynamics of molecules should not be affected since all possible
orderings still correspond to the same plane.
The problem is that I want to check the terms Amber is
calculating by calculating energies for a snapshot of a
molecule. Improper value will be different if different atom
order is used. So I want the ordering to be consistent for
easier comparison. A workaround for this is to sort the atoms in
parameter file so that leap gets the same order every time, but
I would rather want to avoid editing forcefield data files myself.
Also, leap puts quite a lot of effort to have atoms ordered as
in the parameter file, so it would be nice that it got it right
or at least be consistent.
>
> It might also be helpful to the developers if you specify
> the AmberTools version and patch set you are using for
> compiling tleap. I imagine that if you have seen it with
> Glycam, then it may also be present when using other force
> fields.
I have tried it with up-to-date versions of AmberTools 11, 12
and 13. All of them have the same behaviour.
Yes, Glycam is just an example, I expect this to be a general
behaviour for leap.
Reinis
>
> Cheers,
> Karl
>
> ------------------------------------
> Karl N. Kirschner, Ph.D.
> Fraunhofer-Institute for Algorithms
> and Scientific Computing - SCAI
> Department of Bioinformatics
> 53754 Sankt Augustin, Germany
> Tel: +49 (0) 2241-14-2052
> ------------------------------------
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Received on Wed May 08 2013 - 02:30:03 PDT
