#!/usr/bin/perl -w use strict; my $ARGV; my $filein; my $i; my $checkfile; my @sortedkeys; my %NSTEP; my %outarray; my $j; my $outarray; my @f; my $status; my $debug; my $string; my $maxcyc; my $maxcyc10; my $nstep; my $energy; my $rms; my $gmax; my $name; my $number; my $bond; my $angle; my $dihedral; my $vdwaals; my $eel; my $hbond; my $vdw14; my $eel14; my $restraint; my $NSTEP; my $ENERGY; my $RMS; my $GMAX; my $NAME; my $NUMBER; my $BOND; my $ANGLE; my $DIHEDRAL; my $VDWAALS; my $EEL; my $HBOND; my $VDW14; my $EEL14; my $RESTRAINT; my %ENERGY; my %RMS; my %GMAX; my %NAME; my %NUMBER; my %BOND; my %ANGLE; my %DIHEDRAL; my %VDWAALS; my %EEL; my %HBOND; my %VDW14; my %EEL14; my %RESTRAINT; if ($#ARGV < 0) { print " Incorrect usage...\n"; exit; } # Flush the buffer $| = 1; foreach $i ( 0..$#ARGV ) { $filein = $ARGV[$i]; $checkfile = $filein; $checkfile =~ s/\.Z//; if ( $filein ne $checkfile ) { open(INPUT, "zcat $filein |") || die "Cannot open compressed $filein -- $!\n"; } else { open(INPUT, $filein) || die "Cannot open $filein -- $!\n"; } print "Processing sander output file ($filein)...\n"; &process_input; close(INPUT); } print "Starting output...\n"; @sortedkeys = sort {$a <=> $b} keys(%NSTEP); foreach $i ( "NSTEP", "ENERGY", "RMS", "GMAX", "NAME", "NUMBER", "BOND", "ANGLE", "DIHEDRAL", "VDWAALS", "EEL", "HBOND", "VDW14", "EEL14", "RESTRAINT" ) { print "Outputing summary.$i\n"; open(OUTPUT, "> summary.$i"); %outarray = eval "\%$i"; foreach $j ( @sortedkeys ) { print OUTPUT "$j ", $outarray{$j}, "\n"; } close (OUTPUT); } sub process_input { my @f; $status = 0; $debug = 0; while ( ) { $string = $_; next if $string =~ /^\s*$/; # Initialise the output variables undef $bond; undef $angle; undef $dihedral; undef $vdwaals; undef $eel; undef $hbond; undef $vdw14; undef $eel14; undef $restraint; if (/maxcyc.*ncyc/) { @f = split /\s+/, $_; $maxcyc = $f[3]; $maxcyc =~ s/,$//; $maxcyc10 = $maxcyc/10; } if (/NSTEP/) { $_ = ; @f = split /\s+/, $_; $nstep = $f[1]; $energy = $f[2]; $rms = $f[3]; $gmax = $f[4]; $name = $f[5]; $number = $f[6]; if ($debug) { foreach (@f){ print "\"$_\" "; } print "\n"; } else { # Only print every 10% steps if ($nstep % $maxcyc10 == 0) { print "Processing step $nstep of a possible $maxcyc...\n"; } } if ( $debug ) { print $_; print "nstep is $nstep, energy is $energy, rms is $rms, gmax is $gmax, name is $name, number is $number\n"; } $_ = ; $_ = ; if (/BOND.*ANGLE.*DIHED/) { ($bond, $angle, $dihedral) = /BOND.*=(.*\d*\.?\d*).*ANGLE.*=(.*\d*\.?\d*).*DIHED.*=(.*\d*\.?\d*)/; $bond =~ s/^\s*\*+\s*$/99999999.9999/; $angle =~ s/^\s*\*+\s*$/99999999.9999/; $dihedral =~ s/^\s*\*+\s*$/99999999.9999/; if ( $debug ) { print $_; print "bond is $bond, angle is $angle, dihedral is $dihedral\n"; } $_ = ; } if (/VDWAALS/) { ($vdwaals, $eel, $hbond) = /VDWAALS.*=(.*\d*\.?\d*).*EEL.*=(.*\d*\.?\d*).*HBOND.*=(.*\d*\.?\d*)/; $vdwaals =~ s/^\s*\*+\s*$/99999999.9999/; $eel =~ s/^\s*\*+\s*$/99999999.9999/; $hbond =~ s/^\s*\*+\s*$/99999999.9999/; if ( $debug ) { print $_; print "vdwaals is $vdwaals, eel is $eel, hbond is $hbond\n"; } $_ = ; } if (/1-4 VDW/) { ($vdw14, $eel14, $restraint) = /1-4 VDW.*=(.*\d*\.?\d*).*1-4 EEL.*=(.*\d*\.?\d*).*RESTRAINT.*=(.*\d*\.?\d*)/; $vdw14 =~ s/^\s*\*+\s*$/99999999.9999/; $eel14 =~ s/^\s*\*+\s*$/99999999.9999/; $restraint =~ s/^\s*\*+\s*$/99999999.9999/; if ( $debug ) { print $_; print "vdw14 is $vdw14, eel14 is $eel14, restraint is $restraint\n"; } $_ = ; # # check to see if EAMBER is in the mdout file (present when # NTR=1) - removed from process_minout.perl (in process_mdout) # # update arrays $NSTEP{$nstep} = $nstep; $ENERGY{$nstep} = $energy; $RMS{$nstep} = $rms; $GMAX{$nstep} = $gmax; $NAME{$nstep} = $name; $NUMBER{$nstep} = $number; $BOND{$nstep} = $bond; $ANGLE{$nstep} = $angle; $DIHEDRAL{$nstep} = $dihedral; $VDWAALS{$nstep} = $vdwaals; $EEL{$nstep} = $eel; $HBOND{$nstep} = $hbond; $VDW14{$nstep} = $vdw14; $EEL14{$nstep} = $eel14; $RESTRAINT{$nstep} = $restraint; } } } }