* Test case for Monte Carlo with rigid bonds, angles, dihedrals   
* This input file builds N-methyl alanyl acetamide
* using internal coordinates and then manipulates the
* structure based on the dihedrals, bond and agnle ics
* It has been modified to explore the use of the replica/GA command
* for copying multiple (5 structures) structures to explore conformations
* THIS USES MC annealing with translational/rotational degrees of freedom
*
stream datadir.def
open read form unit 1 name @0/toph19.rtf
read rtf card unit 1
open read form unit 1 name @0/param19.prm
read param card unit 1

! Read in the sequence and generate the psf (protein structure file - an
! internal CHARMM data structure describing the specific connectivity for
! the specific structure of interest.  It is created using the information
! from the topology and parameter files
Read sequ card
* maa
*
3
AMN ALA CBX

Generate maa setup !the segment identifier is called maa and the setup
                   !command indicates that the internal coordinate tables
                   !(based upon ic information in the rtf) will be created

ic parameters  !fill the current ic table based upon values from the
               !parameter and/or rtf files

ic seed 1 cl 1 c 1 o  !provide the three atoms to "seed" building

ic build  !build the structure based upon the internal coordinates (ics)

print ic
print coordinates
coor orie  !orient molecule so CM is at origin and principal axes are along
           !cartesian directions

set npar 5 
GAlgorithm SETUp -
    CHROmosomes @npar select segid maa end -
    VARIable_ICs
    DIHEdral INCLude  1 C     2 N     2 CA    2 C   end
    DIHEdral INCLude  2 N     2 CA    2 C     3 N   end
   tran rota
   END   

Nbonds cdie eps 1.0 cutnb 99.0 ctofnb 90.0 wrnmxd 99.0 swit vswit
energy

prnlev 3
GALGorithm EVOLve -
mCarlo   Tbeg 500.0 Tend 250.0  tfrq 10 -
RAND iseed 111 rtran 2.0 rrota 3.6 rdihe 360.0 -
  MAXGenerations 2000 -
  niches 1 inte 10999 -
  gsize 1 muta 1.0  pinte 1.0 qrmin rmin 0.885  -  
  ibig 50 bdis 100.0  -
  print 200 Dist 20.0  delete  clear

skipe bonds
skipe angle
energy 
set 0 0
label loop
incr 0 by 1
inte sele iseg @0 end
if 0 lt @npar goto loop

energy rmin 0.0
print ic
print coor
stop