remarks dgtest1.inp
remarks test metric matrix distrance geometry module -- 
remarks    basic tests on a TRP amino acid 
remarks John Kuszewski and Axel T. Brunger
remarks ==================================

topology reset @CNS_TOPPAR:protein-allhdg5-4.top end   {* this is the DG-version of this file *}

segment
   name="TRYP"
   chain
      @CNS_TOPPAR:protein-allhdg5-4.link
      sequence trp
      end
end
end

parameter 
        @CNS_TOPPAR:protein-allhdg5-4.param 
        nbonds repel = 0.8 end
end

coor
ATOM      1  CA  TRP     1       1.331   1.246   0.096  1.00  0.00      TRYP
ATOM      2  HA  TRP     1       1.571   0.780   1.039  1.00  0.00      TRYP
ATOM      3  CB  TRP     1       2.535   2.085  -0.418  1.00  0.00      TRYP
ATOM      4  HB1 TRP     1       2.239   2.586  -1.319  1.00  0.00      TRYP
ATOM      5  HB2 TRP     1       2.751   2.850   0.315  1.00  0.00      TRYP
ATOM      6  CG  TRP     1       3.804   1.229  -0.669  1.00  0.00      TRYP
ATOM      7  CD1 TRP     1       4.717   0.866   0.299  1.00  0.00      TRYP
ATOM      8  HD1 TRP     1       4.659   1.099   1.355  1.00  0.00      TRYP
ATOM      9  CD2 TRP     1       4.351   0.653  -1.938  1.00  0.00      TRYP
ATOM     10  NE1 TRP     1       5.724   0.123  -0.275  1.00  0.00      TRYP
ATOM     11  HE1 TRP     1       6.486  -0.256   0.211  1.00  0.00      TRYP
ATOM     12  CE2 TRP     1       5.557  -0.035  -1.629  1.00  0.00      TRYP
ATOM     13  CE3 TRP     1       3.937   0.642  -3.303  1.00  0.00      TRYP
ATOM     14  HE3 TRP     1       3.030   1.139  -3.603  1.00  0.00      TRYP
ATOM     15  CZ2 TRP     1       6.307  -0.689  -2.607  1.00  0.00      TRYP
ATOM     16  HZ2 TRP     1       7.219  -1.201  -2.337  1.00  0.00      TRYP
ATOM     17  CZ3 TRP     1       4.699  -0.019  -4.279  1.00  0.00      TRYP
ATOM     18  HZ3 TRP     1       4.371  -0.014  -5.308  1.00  0.00      TRYP
ATOM     19  CH2 TRP     1       5.879  -0.680  -3.932  1.00  0.00      TRYP
ATOM     20  HH2 TRP     1       6.459  -1.186  -4.691  1.00  0.00      TRYP
ATOM     21  C   TRP     1       0.137   2.181   0.303  1.00  0.00      TRYP
ATOM     22  O   TRP     1      -0.629   2.346  -0.631  1.00  0.00      TRYP
ATOM     23  OXT TRP     1       0.010   2.715   1.393  1.00  0.00      TRYP
ATOM     24  N   TRP     1       0.945   0.198  -0.894  1.00  0.00      TRYP
ATOM     25  HT1 TRP     1       1.555  -0.635  -0.775  1.00  0.00      TRYP
ATOM     26  HT2 TRP     1       1.057   0.571  -1.858  1.00  0.00      TRYP
ATOM     27  HT3 TRP     1      -0.048  -0.074  -0.740  1.00  0.00      TRYP
END

topology 

   pres dimp
      delete improper HB1 HB2 CA CG 
      delete improper HT1 HT2 CA HT3
   end
end

patch dimp  reference=nil=( all ) end
 
coor copy end

flags include noe cdih end

{* scale the energies to reduce precision dependencies of the output *}
igroup 
    interaction ( all ) ( all ) 
        weight bond 0.001
	       angl 0.001
	       impr 0.001
	       dihe 0.001
	       vdw  0.001 
	       elec 0.001 
	end 
end
 
energy end

{* =============================================================== *}
{*    test 1: generate all possible distances and store as NOEs    *}
{* =============================================================== *}
set display prenoes.dat end

set message=off end
set echo=off end
for $hy1 in id ( all ) loop hy1
   for $hy2 in id ( all ) loop hy2
        if ($hy1 # $hy2 ) then 
   
           pick bond (id $hy1) (id $hy2) geometry
	
           display assign (id $hy1) (id $hy2) 
	   display        $result 0.01 0.01
	end if
   end loop hy2
end loop hy1
                                 
close prenoes.dat end

noe 
   nres=2000 
   class all @prenoes.dat
end
set message=on end
set echo=on end

set seed=12345 end

mmdg
        verbose off
        iacc=5. tacc=5. bacc=0.2 pacc=5. 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

set message=off end   coor fit end    set message=on end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 2: generate all non-h distances and store as NOEs       *}
{* =============================================================== *}
set display prenoes.dat end

set message=off end
set echo=off end
for $hy1 in id ( not hydrogen ) loop hy1
   for $hy2 in id ( not hydrogen ) loop hy2
        if ($hy1 # $hy2 ) then 
   
           pick bond (id $hy1 ) (id $hy2 ) geometry
	
           display assign (id $hy1) (id $hy2) 
	   display        $result 0.01 0.01
	end if
   end loop hy2
end loop hy1
                                 
close prenoes.dat end

noe 
   reset
   nres=2000 
   class all @prenoes.dat
end
set message=on end
set echo=on end

set seed=12345 end

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5.
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

set mess=off end   coor fit sele=( not hydro ) end  set mess=on end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 3: use "realistic" NOE data set                         *}
{* =============================================================== *}
set display prenoes.dat end

set message=off end
set echo=off end
for $hy1 in ("HA" "HB1" "HB2" "HD1" "HE1" "HE3" "HZ2" "HZ3" "HH2") loop hy1
   for $hy2 in ("HA" "HB1" "HB2" "HD1" "HE1" "HE3" "HZ2" "HZ3" "HH2") loop hy2
        if ($hy1 # $hy2 ) then 
           pick bond (name $hy1) (name $hy2) geometry
           evaluate ($dnoe = $result)
           if ($dnoe < 2.8) then
                  evaluate ($value = 2.8)
                  evaluate ($errpl = 0.2)
                  evaluate ($errmn = 1.4)
           elseif ($dnoe < 3.4) then
                  evaluate ($value = 3.4)
                  evaluate ($errpl = 0.3)
                  evaluate ($errmn = 1.2)
           elseif ($dnoe < 4.0) then
                  evaluate ($value = 4.0)
                  evaluate ($errpl = 0.5)
                  evaluate ($errmn = 1.7)
           end if
           if ($dnoe < 4.0) then
                display assign (resid 1 and name $hy1)
                display (resid 1 and name $hy2) $value $errmn $errpl
           end if
	end if
   end loop hy2
end loop hy1
                                 
close prenoes.dat end

noe 
   reset
   nres=2000 
   class all @prenoes.dat
end
set message=on end
set echo=on end

set seed=12345 end

mmdg
        verbose off
        iacc=5. tacc=5. bacc=0.2 pacc=5.
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

set message=off end   coor fit end    set message=on end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 4: test the "rigid" group option                        *}
{* =============================================================== *}

set seed=12345 end

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
	group=( all ) 0.1 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

set message=off end   coor fit end    set message=on end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 4b: test the "rigid" group option with two groups       *}
{* =============================================================== *}

set seed=12345 end

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
	group=( not hydrogen ) 0.1 
	group=( hydrogen ) 0.1 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

coor fit sele=( not hydro )  end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 4c: test substructures                                  *}
{* =============================================================== *}

set seed=12345 end

do (refx=x) ( all )
do (refy=y) ( all )
do (refz=z) ( all )

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
	group=( not hydrogen ) 0.01 
	group=( hydrogen ) 0.01 
	substructure=( not hydrogen ) 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (not hydrogen)
do (y = y * $dgscale) (not hydrogen)
do (z = z * $dgscale) (not hydrogen) 

set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

do (z=-z) ( all )
set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 4d: test substructures with storage in memory           *}
{* =============================================================== *}

set seed=12345 end

do (refx=x) ( all )
do (refy=y) ( all )
do (refz=z) ( all )

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
	group=( not hydrogen ) 0.01 
	group=( hydrogen ) 0.01 
	storebounds
end

set seed=12345 end

mmdg
        recallbounds
	substructure=( not hydrogen ) 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (not hydrogen)
do (y = y * $dgscale) (not hydrogen)
do (z = z * $dgscale) (not hydrogen) 

set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

do (z=-z) ( all )
set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

set seed=12345 end

mmdg
        recallbounds
	substructure=( not hydrogen ) 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (not hydrogen)
do (y = y * $dgscale) (not hydrogen)
do (z = z * $dgscale) (not hydrogen) 

set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

do (z=-z) ( all )
set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

coor swap end
coor copy end


{* =============================================================== *}
{*    test 4e: test substructures with storage in file             *}
{* =============================================================== *}

set seed=12345 end

do (refx=x) ( all )
do (refy=y) ( all )
do (refz=z) ( all )

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
	group=( not hydrogen ) 0.01 
	group=( hydrogen ) 0.01 
	writebounds=dgtest1.dat
end

set seed=12345 end

mmdg
        readbounds=dgtest1.dat
	substructure=( not hydrogen ) 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (not hydrogen)
do (y = y * $dgscale) (not hydrogen)
do (z = z * $dgscale) (not hydrogen) 

set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

do (z=-z) ( all )
set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

set seed=12345 end

mmdg
        readbounds=dgtest1.dat
	substructure=( not hydrogen ) 
        random 
        metrize (all) 100
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (not hydrogen)
do (y = y * $dgscale) (not hydrogen)
do (z = z * $dgscale) (not hydrogen) 

set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

do (z=-z) ( all )
set mess=off end   coor fit sele=( not hydro ) end  set mess=on end

coor swap end
coor copy end


{* =============================================================== *}
{*    test 5: test partial metrization                             *}
{* =============================================================== *}

set seed=12345 end

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
        random 
        metrize (all) 4
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

set message=off end   coor fit end    set message=on end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 6: test ordered metrization                             *}
{* =============================================================== *}

set seed=12345 end

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
        ordered 
        metrize (all) 4
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

set message=off end   coor fit end    set message=on end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 7: test no metrization                                  *}
{* =============================================================== *}

set seed=12345 end

mmdg
        verbose off
	iacc=5. tacc=5. bacc=0.2 pacc=5. 
	?
end

set display=OUTPUT end
display $embedded
display $non_met_gap
display $dgscale

do (x = x * $dgscale) (all)
do (y = y * $dgscale) (all)
do (z = z * $dgscale) (all) 

energy end
evaluate ($chi_ener=$impr) 
do (z=-z) ( all )
energy end
if ($impr > $chi_ener) then
   do (z=-z) ( all )
end if

set message=off end   coor fit end    set message=on end
coor rms end
do (b=rmsd ) ( all )
write coords end

coor swap end
coor copy end

{* =============================================================== *}
{*    test 8: test pseudoatom correction                           *}
{* =============================================================== *}

do (refx=x) ( all )
do (refy=y) ( all )
do (refz=z) ( all )

noe
  reset
  nres=100
  assign ( name hb* ) ( name ca )  4. 1. 2.
  assign ( name ca  ) ( name hb* ) 7. 1. 2.  
  assign ( name hb* ) ( name ht* )  8. 1. 2. 
end

flags exclude * include noe end

mmdg
   verbose=on
   storebounds
end

stop