* CHARMM command stream file to compute contact map for
* structures of calcium binding proteins
*

!reads the topology file
open unit 1 read form name "$toppar/top_all22_prot.inp"
read rtf card unit 1
close unit 1

!reads the paramter file
open unit 1 read form name "$toppar/par_all22_prot.inp"
read param card unit 1
close unit 1

!reads sequence file
open unit 1 read form name camn.seq
read sequ card unit 1
close unit 1

generate 1CFC setup

!defines the backbone atoms as a type
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

!defines the sidechain atoms as a type
define side select ( (.not. bb) ) end

!loops through and reads the coordinates and generates the distance maps
set model 1
label readmodel

!  get coordinates

if @model gt 9 goto l1
open unit 1 read form name "camn_apo_00@MODEL.chm.pdb"
goto read
label l1
open unit 1 read form name "camn_apo_0@MODEL.chm.pdb"
label read
read coor pdb unit 1
close unit 1

if model gt 9 goto w1
open unit 1 write form name "camn_apo_00@MODEL.dmap"
goto title
label w1
open unit 1 write form name "camn_apo_0@MODEL.dmap"
*defines title to be printed at the top of output distance map files and
*then generates map.  Cutoff is the number to change for different amounts of info 
label title
title
*  Distance matrix for structure 1cfc model @model
*
coor dmat single residue unit 1 cutoff 500.0 -
     select ( side ) end  -
     select ( side ) end

incr model by 1
if model le 25 goto readmodel

stop