- CARNAL -
			  AMBER  4.1

		      COORDINATE  ANALYSIS


input stdin 
> # RMS deviation of moving part of solute
> FILES_IN
>   PARM   p1 stbtcap.top;
Reading parm file (stbtcap.top)
parm: opening stbtcap.top
stbtcap.top title:
                                                                                
>   STREAM s1 traj/md01.crd;
Using default parm (stbtcap.top) for STREAM s1
stream: opening traj/md01.crd
> FILES_OUT
>   TABLE  t1 md01.rms;
> DECLARE
>   GROUP  g1 (RES 5-17,25,27-44,59-81,89-101,104,105,107-119,
Using default stream
> 	     142,163-170,172,174-181,195-201,212-214,
> 	     216,228,230,333-336,338-350,438,448-450,
> 	     468-470,472,479); 
** Group g1: 2117 atoms
>   RMS    r1 g1;
RMS: comparing default stream to its initial set
>   GROUP  g2 ((GROUP g1) & (ATOM NAME C CA N));
Using default stream
** Group g2: 417 atoms
>   RMS    r2 g2;
RMS: comparing default stream to its initial set
>   GROUP  g3 (RES 479);
Using default stream
** Group g3: 31 atoms
>   RMS    r3 g3;
RMS: comparing default stream to its initial set
>   RMS    r4 FIT g3;
RMS: comparing default stream to its initial set
> OUTPUT
>   TABLE  t1 r1 r2 r3 r4;
> END      
(EOF reached on traj/md01.crd)
STREAM s1: no more files/crds (iteration 150)
SUMMARY
--RMS r1: avg       0.926  dev     0.141  max    1.058  min    0.137  N 149
--RMS r2: avg       0.610  dev     0.103  max    0.744  min    0.082  N 149
--RMS r3: avg       0.691  dev     0.157  max    1.017  min    0.131  N 149
--RMS r4: avg       0.242  dev     0.054  max    0.420  min    0.103  N 149