ffld_server Command Help

Command: $SCHRODINGER/utilities/ffld_server

Assign force field parameters to structures
ffld_server -i<format> <input_filespec> [more options]
-imae|-imol2|-isdf|-ipdb    <infile>     Input structure file
-omae|-omol2|-osdf    <outfile>    Treated output file (optional)
-store_initial_structure          Copy input struct to output file
-o_skipped           <maefile>    Save problematic struct in Mae file
-version             <number>     Force field version specifier
-charges_from_ct                  Use partial charges supplied in input
-types_to_ct                      Record atom types in output CT
-print_parameters                 Print force field parameter values
-print_details                    Add some details to parameter listing
-print_energy_components          Print all detailed energy components 
-print_total_energy          Print the total energy for each CT 
-out_file           <outputfile>  Direct output into file
-plan_sc_ena                      Enable scaling of forces for planarity
-plan_sc_tors        <factor>     Planarity scale factor for prop torsions
-plan_sc_impr        <factor>     Planarity scale factor for impr torsions
-plan_sc_bend        <factor>     Planarity scale factor for imp tor bends
-enhanced_planar_typer            filename with specific rules to enforce planarity
-enhanced_planar_exclude_ct1      exclude centers with CT1 atom neighbors from enforce planarity
-sgbnp      generate SGB/NP parameters
-bend_conj_amines                 Use bend conjugated amines as provided by QM
-bend_conj_amines_in_cm1abcc      Use bend conjugated amines in CM1A-BCC protocol
-print_parameters_cm1bcc          Print parameters in structure preparation
-no_cm1a_bcc                      Do not calculate CM1A_BCC charges
-no_cgen_in_cm1bcc                Skip conf gen in CM1A_BCC protocol
-no_str_cleanup_cm1bcc            No minimization after cgen in CM1A_BCC protocol
-use_strprep_geom                 use geometry generated by the structure preparation protocol (f16 only)
-nosym_charge_in_cm1bcc           disable the charge symmetrization in CM1A_BCC protocol
-skip_1Dto3D                      Skip the 1D to 3D conversion step in the structure preparation protocol
-skip_premin_with_skip_1Dto3D     skip the minimization before the conformation generation step (requires -skip_1Dto3D)
-require_str_prep                 Require successful structure preparation in CM1A_BCC protocol
-no_mmnddo_in_cm1bcc              No mmnddo calc in CM1A_BCC protocol
-cm1bcc_required                  Require successful CM1A_BCC calculation
-cgen_mae            <maefile>    Save mmffld_conf struct in Mae file
-cgen_mae_separate_files           Save mmffld_conf struct in individual files
-opt                              Enable optimization
-max_step            <number>     Maximum number of opt steps allowed
-dielectric      <dielectric>     Dielectric constant
-cutoff              <radius>     Cutoff radius in Angstroms
-grad                <value>      Gradient convergence criterion
-energy              <value>      Energy change convergence criterion
-min_verbose         <level>      Minimizer reporting verbosity
-min_perturb                      Perturb coordinates before minimizing
-line_search_method         <method>      Set the line search method in minimization
-no_ele                           Do not use electrostatics
-lj_repulsive_only                Repulsive only for L-J interactions > 1,4
-enable_metal_force_field         Enable metal force field
-metal_ff_type          <type>    Metal FF type: LFMM(0), AOM(1), Morse(2), Dummy(3)
-metal_ligand_cutoff  <radius>    Metal-ligand cutoff radius in Angstroms
-metal_metal_cutoff   <radius>    Metal-metal cutoff radius in Angstroms
-CG|-BFGS                         Use Conjugate Gradient or BFGS optimizer
-rest_file          <restfile>    File giving position/torsion restraints, constraints
-print_restraints                 Print any position/torsion restraints
-ifo                 <number>     Lewis structure operation code
-verbose             <level>      Lewis operation report verbosity
-delete_dummies                   Lewis operation deletes dummy atoms
-h                                Show terse usage message
-hh                               Show longer usage message