AMBER Archive (2004)

Subject: AMBER: CARNAL- movement of an axis

From: Wen Li (liw_at_wadsworth.org)
Date: Thu Jun 03 2004 - 15:34:11 CDT

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:

FILES_IN
 PARM p1 topo;
 STREAM s1 trajectory;
 STATIC refset initial_coords;

DECLARE
 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;

OUTPUT
 TABLE tab1 angle;

END

Thanks,
Wen
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