file: tutorial.two



Minimizing the energy  and writing coordinates with ECEPPAK
-----------------------------------------------------------


We can easily  extend the example provided in tutorial.one (a 10-residues  chain of 
L-alanine) were we computed the energy to obtain a locally-minimized conformation.


1- Generate an input file with suffix "inp" ( i.e., ten_ala_min.inp) that will contain
 the instructions for ECEPPAK

2.-   Include in ten_ala_min.inp  the $CNTRL Data Group to define the type of run and
ask the program to provide the coordinates corresponding final conformation in PDB format.

$CNTRL
runtyp = minimize    ! run type is a minimization
PRINT_CART             !  print Cartesian coordinates
OUTFORMAT   =PDB       !  format of the Cartesian file is PDB
 FILE  = ala10M     !    prefix of the PDB file is  ala10M
$END

3.-  Include in ten_ala_min.inp  the $SEQ data group with the amino acid sequence.
Let try a  different manner and write the sequence using a three-letter code.
Since this form of sequence specification is not the default we have  to use and extra 
keyword in the $CNTRL  data group, we  should add: " res_code= three_letter". 

Now let's input the sequence
we'll use  again the AMINO-COCH3 and CARBOXYL-NHCH3 at the N- and  C-terminus, 
respectively. 
The two end groups must be also specified using a three-letter code (see manual 
for one-letter and three letter codes for residues and end groups).

The 

The $SEQ data group reads, 


$SEQ
ACE
ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA
NME
$END


4.- Finally, we include in ten_ala_min.inp  the $GEOM data group  the set of dihedral 
angles defining the conformation of the polypeptide chain.
As before, we specify an alpha-helical conformation. 

The $GEOM data group reads,

$GEOM
 180.000 180.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 180.000
$END
 

5.- The complete file now  reads,

$CNTRL
runtyp = minimize    ! run type is a minimization
PRINT_CART             !  print Cartesian coordinates
OUTFORMAT   =PDB       !  format of the Cartesian file is PDB
 FILE  = ala10M     !    prefix of the PDB file is  ala10M

res_code= three_letter   ! use three-letter code to specify input sequence
$END

$SEQ
ACE
ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA
NME
$END

$GEOM
 180.000 180.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 -66.000 -40.000 180.000  60.000
 180.000
$END





6.- Save the file and run ECEPPAK


In the command line type:
    
     recepp.s ENERGY ten_ala_min TEN_ALA_MIN x x  1

7.- The output of the program is written in three separate files:

(a) main_out.TEN_ALA_MIN with a description of the results of the energy 
    minimization procedure, 

(b) outo.TEN_ALA_MIN a file that is usually used for other calculations
    with ECEPPAK, containing the different energy terms, the sequence
    (in ECEPP format) and the list of final dihedral angles, and

(c) ala10M.pdb  a file containing the Cartesian coordinates
    of the energy-minimized conformation.

The total energy of the molecule in the energy-minimized conformation is: 

                ETOT    -0.218730E+02   (total)

Since the minimization process use parameters that are machine-specific
different energy values may be obtained in different computers.