* CHARMM command stream file to compute contact map for
* structures of calcium binding proteins.  This file
* adds hydrogens and minimizes the hydrogens before
* computing the contact map
*

open unit 1 read form name "$toppar/top_all22_prot.inp"
read rtf card unit 1
close unit 1

open unit 1 read form name "$toppar/par_all22_prot.inp"
read param card unit 1
close unit 1

open unit 1 read form name camn.seq
read sequ card unit 1
close unit 1

generate 1CLL setup

define bb select ( type ca .or. type n .or. type c .or. type o -
                 .or. type ha .or. type ht1 .or. type ht2 .or. type ht3 ) end

define side select ( (.not. bb) ) end


!  get coordinates

open unit 1 read form name "camn_ca.pdb"
read coor pdb unit 1
close unit 1

! add hydrogens

hbuild

!copy coordinates for future comparison
coor copy comp

!minimize (ala B. Dominy)

cons fix select .not. hydrogen end
minimize ABNR nstep 2000 step 1.0 tole 0.001

coor rms comp select all end

open unit 1 write form name "camn_ca.dmap"
title
*  Distance matrix for structure 1cll
*
coor dmat single residue unit 1 cutoff 500.0 -
     select ( side ) end  -
     select ( side ) end

stop