tutorial.two

file: tutorial.two

Minimizing the energy and writing coordinates with ECEPPAK
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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

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

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.