&FORCE_EVAL ! This section defines method for calculating energy and forces METHOD FIST ! Using Molecular Mechanics &MM &FORCEFIELD ! This section specifies forcefield parameters parm_file_name ace_ala_nme.pot ! This file contains force field parameters parmtype CHM ! forcefield parameters has CHARMM format &SPLINE ! This section specifies parameters to set up the splines used ! in the nonboned interactions (both pair body potential and many body potential) EMAX_SPLINE 1.0 ! Specify the maximum value of the potential up to which splines will be constructed &END &END FORCEFIELD &POISSON ! This section specifies parameters for the Poisson solver &EWALD ! This section specifies parameters for the EWALD summation method (for the electrostatics) EWALD_TYPE ewald ! Standard non-fft based ewald method ALPHA .36 GMAX 29 ! Number of grid points &END EWALD &END POISSON &PRINT ! This section controls printing options &FF_INFO &END &FF_PARAMETER_FILE &END &END &END MM &SUBSYS ! This section defines the system &CELL ! Unit cell set up ABC 50.0 50.0 50.0 ! Lengths of the cell vectors A, B, and C &END CELL &COLVAR ! This section specifies collective varialbe &TORSION ! This section defines variable as torsion angle ATOMS 5 7 9 15 ! Four atoms specify torsion angle &END &PRINT &END &END &COLVAR ! This section specifies collective varialbe &TORSION ! This section defines variable as torsion angle ATOMS 7 9 15 17 ! Four atoms specify torsion angle &END &PRINT &END &END &TOPOLOGY CONN_FILE_NAME ace_ala_nme.psf ! File which contains the connectivity information CONNECTIVITY psf ! Format of the connectivity file is PSF COORD_FILE_NAME ini.pdb ! File which contains atom's coordinates of the system COORDINATE PDB ! Coordinates are in the PDB format &DUMP_PDB ! This sections specifies the dumping of the PDB at the starting geometry &END &DUMP_PSF ! This sections specifies the dumping of the PSF connectivity &END &END TOPOLOGY &PRINT &TOPOLOGY_INFO AMBER_INFO &END &END &END SUBSYS &END FORCE_EVAL &GLOBAL ! Section with general information regarding which kind of simu lation to perform an parameters for the whole PROGRAM PRINT_LEVEL LOW ! Global print level PROJECT ch ! Name of the project. This word will appear as part of a name of all ouput files (except main ouput file, specified with -o option) RUN_TYPE GEO_OPT ! Run type is a geometry optimization &END GLOBAL &MOTION ! This section specifies a set of tool connected with the motion of the nuclei &CONSTRAINT ! Section specifying information regarding how to impose constraints on the system &COLLECTIVE INTERMOLECULAR T COLVAR 1 ! Sequential number of the variable &RESTRAINT ! This section specifies how stong is the restraint K=5.0 ! U(x)=K*(x-x0)^2 &END TARGET [deg] _A1_ ! _A1_ will be changed to the number by an external scritp &END &COLLECTIVE INTERMOLECULAR T COLVAR 2 ! Sequential number of the variable &RESTRAINT ! This section specifies how stong is the restraint K=5.0 ! U(x)=K*(x-x0)^2 &END TARGET [deg] _A2_ ! _A1_ will be changed to the number by an external scritp &END &END &PRINT ! This section controls the printing properties during an optimization or MD run &TRAJECTORY FORMAT PDB ! Format of the ouput trajectory is PDB ADD_LAST NUMERIC ! (Wiki) If the last iteration should be added, and if it should be marked symbolically (with l) or with the iteration number.Not every iteration level is able to identify the last iteration early enough to be able to output. When this keyword is activated all iteration levels are checked for the last iteration step. &EACH GEO_OPT 100 ! Print one frame every 100 iteration &END &END &END &GEO_OPT ! This section specifies optimizer options OPTIMIZER BFGS ! Type of the optimizer MAX_ITER 5000 ! Maximum number of optimization steps MAX_FORCE 0.005 ! The value of maximal force RMS_FORCE 0.003 ! The value of maximal force RMS &END &END