<html><head><meta name="color-scheme" content="light dark"></head><body><pre style="word-wrap: break-word; white-space: pre-wrap;">#!/bin/tcsh

mkdir outliers
cd outliers

cat &lt;&lt; EOF &gt; process-outliers.perl 
#!/bin/perl

open IN, "&lt; ../suite1.dat";
open OUT1, "&gt; pt-outliers.in";
open OUTtrig, "&gt; trigframes.dat";
open OUToutlier, "&gt; outlierframes.dat";

print OUT1 "parm ../../../build/noWAt.topo.hmr\n\n";

\$trigframe = 0;
\$oriframe = 0;
while (&lt;IN&gt;) {
        \$oriframe = \$oriframe + 1;
        @line = split " ",$_;
        if ((\$line[2] eq "!!") || (\$line[1] eq "!!")) {
                \$trigframe = \$trigframe + 1;
                print OUT1 "trajin ../298.nc start \$oriframe stop \$oriframe \n";
        }
        if ((\$line[2] eq "!!") &amp;&amp; (\$line[0] ne "trig")) {print OUToutlier "\$trigframe   \$line[6]\n";}
        if (\$line[0] eq "trig") {print OUTtrig "\$trigframe       \$line[3]\n";}

}
print OUT1 "\nautoimage origin\n";
print OUT1 "rmsd :2 first\n";
print OUT1 "\ntrajout trig.nc\n";
EOF

cat &lt;&lt; EOF &gt; pt-analysis1.in
parm ../../../build/noWAt.topo.hmr

trajin trig.nc

reference ../../../../../../A-form.pdb [a-form]

rmsd rms_2_aform :1,2&amp;!@H= ref [a-form] mass

distance dist_sugar_ox :1@O2' :2@O4'
distance dist_N3-O5p :1@N3 :1@O5'
distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6

dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3'  type gamma
dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3'  type delta
dihedral e1 :1@C4' :1@C3' :1@O3' :2@P    type epsilon
dihedral z1 :1@C3' :1@O3' :2@P   :2@O5'  type zeta
dihedral c1 :1@O4' :1@C1' :1@N9  :1@C4   type chin

dihedral a2 :1@O3' :2@P   :2@O5' :2@C5'  type alpha
dihedral b2 :2@P   :2@O5' :2@C5' :2@C4'  type beta
dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3'  type gamma
dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3'  type delta
dihedral c2 :2@O4' :2@C1' :2@N9  :2@C4   type chin
run

avg rms_2_aform out avg-rmsd-all.dat
hist rms_2_aform,0,5,0.1 out rmsd-hist.dat name RMSD norm
hist COM,0,10,0.1 out COM-hist.dat name CoM norm
hist dist_sugar_ox,0,10,0.1 out distO2O4-hist.dat norm
hist dist_N3-O5p,0,10,0.1 out distN3-O5p-hist.dat norm
hist rms_2_aform,0,5,0.1 dist_sugar_ox,0,10,0.1 out 2dhist_rms-dist.gnu norm
hist g1,-180,180,1 out dihed_g1-hist.dat name gamma_1 norm
hist d1,-180,180,1 out dihed_d1-hist.dat name delta_1 norm
hist e1,-180,180,1 out dihed_e1-hist.dat name epsilon_1 norm
hist z1,-180,180,1 out dihed_z1-hist.dat name zeta_1 norm
hist c1,-180,180,1 out dihed_c1-hist.dat name chi_1 norm
hist a2,-180,180,1 out dihed_a2-hist.dat name alpha_2 norm
hist b2,-180,180,1 out dihed_b2-hist.dat name beta_2 norm
hist g2,-180,180,1 out dihed_g2-hist.dat name gamma_2 norm
hist d2,-180,180,1 out dihed_d2-hist.dat name delta_2 norm
hist c2,-180,180,1 out dihed_c2-hist.dat name chi_2 norm
EOF

cat &lt;&lt; EOF &gt; pt-hb-rna.in
parm ../../../build/noWAt.topo.hmr

trajin trig.nc

autoimage origin

hbond :1-2 avgout avghb-rna.dat printatomnum
EOF

perl process-outliers.perl
cpptraj -i pt-outliers.in &gt; pt-outliers.log 
cpptraj -i pt-analysis1.in &gt; pt-analysis1.log
cpptraj -i pt-hb-rna.in &gt; pt-hb-rna.log
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