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.