#
# XBY6: ANALYZE THE ATOM RMS FIT FOR THE 10 MINIMIZED CLUSTERS
#                       D.E. VOLK  09/18/00
FILES_IN
  PARM p1 all.top;
#
  STREAM s1 mincluster1.restrt mincluster2.restrt
            mincluster3.restrt mincluster4.restrt
            mincluster5.restrt mincluster6.restrt
            mincluster8.restrt mincluster7.restrt
            mincluster9.restrt mincluster10.restrt;
#
#
#STATIC ref NOBOX ATOM 797 mincluster538.restrt;
#
FILES_OUT
# 
  COORD c1 aveminclusters.inpcrd RST;
#
DECLARE
# Define GUA & DG -
  GROUP gg1 ((ATOM NAME C5' C4' C3' C2' C1' O4' O3' O5' 
                        N9 C8 N7 C5 C6 O6 N1 C2 N2 N3 C4) 
         &  (RES 4, 5, 7, 15, 17, 18, 25, 28));  
# Define ADE & DA -
  GROUP ga1 ((ATOM NAME C5' C4' C3' C2' C1' O4' O3' O5' 
                        N9 C8 N7 C5 C6 N6 N1 C2 N3 C4) 
         &  (RES 3, 6, 8, 13, 19, 20));  
# Define THY  & DT -
  GROUP gt1 ((ATOM NAME C5' C4' C3' C2' C1' O4' O3' O5' 
                        N1 C6 C5 C7 C4 O4 N3 C2 O2)
         &  (RES 9, 10, 16, 21, 23, 26));  
# Define CYT & DC -
  GROUP gc1 ((ATOM NAME C5' C4' C3' C2' C1' O4' O3' O5' 
                        N1 C6 C5 C4 N4 N3 C2 O2)
         &  (RES 1, 2, 11, 12, 14, 22, 24, 25));  
# Define group P atoms
  GROUP gp1  (ATOM NAME P O1P O2P S1P S2P);
# Define All Heavy Atoms -
  GROUP gall (GROUP gg1 ga1 gt1 gc1 gp1);
#
  RMS fit1 FIT gall s1;
#
OUTPUT
  COORD c1 fit1 AVERAGE;
END