AMBER Archive (2004)

Subject: Re: AMBER: CARNAL- movement of an axis

From: Bill Ross (
Date: Thu Jun 03 2004 - 15:53:47 CDT

You have 2 axes defined on different snapshots of a molecule.
The angle between those axes would be a combined measure of the
tumbling and bending motions of the molecule, probably not what
you want.


> I tried to find angular changes of a helix through an MD trajectory
> relative to its initial position. I wonder what should be corrected in
> the following carnal input:
> PARM p1 topo;
> STREAM s1 trajectory;
> STATIC refset initial_coords;
> GROUP grp1 (RES 5-10);
> GROUP grp2 (RES 20-25);
> AXIS ax1 grp1%cmass s1 grp2%cmass s1;
> AXIS ax2 grp1%cmass refset grp2%cmass refset;
> ANGLE angle ax1 ax2;
> TABLE tab1 angle;
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