@TIW ################################################################################ # Command file for TI simulation setup ################################################################################ # Location of input and output directories / file(s) # # lig_struct_path: Folder containing the ligand input file(s) # output_path: Basis directory in which all setup and analysis folders will # be generated. The directory must be identical with the # 'output_path' directory used for setup of the MD simulations. lig_struct_path /home/user/tutorial/structs output_path /home/user/tutorial ################################################################################ # Parameters required for TI simulation setup: # The following parameters have to be specified and need to be identical # in all subsequent runs for one system / TI-setup # # ti_simulation_setup: Request setup of TI simulation # charge_method: Charge method that shall be used, either "resp" or "am1" # lig_name_v0_struct: Name of start-ligand - Must be identical to the name of # the file in the "structs" folder used for generation of # parameter and library files with the common MD setup # functionality of FEW. # lig_name_v1_struct: Name of end-ligand - Must be identical to the name of # the file in the "structs" folder used for generation of # parameter and library files with the common MD setup # functionality of FEW. # lig_alias_v0: Alias that shall be used for the identification of the # start-ligand. The alias must consist of 3 characters. # lig_alias_v1: Alias that shall be used for the identification of the # end-ligand. The alias must consist of 3 characters. # softcore_mask_v0: Soft core atom mask for start-structure, specifying the # atoms of the start-structure (state V0) that shall be # regarded as soft core using the format # @ # softcore_mask_v1: Soft core atom mask for end-structure, specifying the # atoms of the end-structure (state V1) that shall be # regarded as soft core using the format # @ ti_simulation_setup 1 charge_method am1 lig_name_v0_struct L51c lig_name_v1_struct L51d lig_alias_v0 LFc lig_alias_v1 LFd softcore_mask_v0 LFc@C14,H1 softcore_mask_v1 LFd@N3 # ################################################################################ # 1) Parameters for preparation of coordinate and topology files of solvated # systems of start- and end-structures for TI simulations # # A) Generation of atom association list based on ligand mol2 files of # start and end structures # # prepare_match_list: Request creation of matching list prepare_match_list 1 # # B) Setup of coordinate and topology files # # It is required that RESTRT (coordinate) and topology files for the ligand and # complex of the start structure exist. These can be generated with the common # MD setup functionality of FEW. # # prepare_inpcrd_prmtop: Request setup of coordinate and topology files # lig_inpcrd_v0: Coordinate file (restart file) of ligand - start structure # com_inpcrd_v0: Coordinate file (restart file) of complex - start structure # lig_prmtop_v0: Topology of ligand - start structure # com_prmtop_v0: Topology of complex - start structure # match_list_file: Optional: File containing the atom association information # for the common part of start- and end-structures. Must only # be specified if step 1A was not successful and the list was # created manually. # chain_termini: Comma separated numbers of terminal residues of chains in # receptor structure. # create_sybyl_mol2: Request generation of mol2-files with sybyl atom types # for easy comparison of atom names of start- and end- # structures. Can facilitate checking and manual adjustment # of atom names in the end-structure, if automatic matching # is not successful. # additional_library: If an additional library file is required, e.g. for # non-standard residues present in the receptor structure, # this file must be specified here. # additional_frcmod: If additional parameters are needed, e.g. for describing # non-standard residues present in the receptor structure, # a parameter file should be provided here. # SSbond_file: File with disulfide bridge definitions # prepare_inpcrd_prmtop 1 lig_inpcrd_v0 /home/user/tutorial/MD_am1/L51c/lig/equi/md_nvt_red_06.restrt com_inpcrd_v0 /home/user/tutorial/MD_am1/L51c/com/equi/md_nvt_red_06.restrt lig_prmtop_v0 /home/user/tutorial/MD_am1/L51c/cryst/L51c_solv_lig.top com_prmtop_v0 /home/user/tutorial/MD_am1/L51c/cryst/L51c_solv_com.top match_list_file chain_termini 235 create_sybyl_mol2 1 additional_library /home/user/tutorial/input_info/CA.lib additional_frcmod SSbond_file /home/user/tutorial/input_info/disulfide_bridges.txt # 2) Setup scripts for TI MD # # General parameters # # no_shake: Set to "1", if no SHAKE shall be performed # ti_batch_path: Root path to be used in setup of batch files # ti_prod_template: Template script for TI production simulations no_shake 1 ti_batch_path /home/user/tutorial ti_prod_template /home/user/tutorial/input_info/MD_prod_noShake_TI.in # # A) Setup of scripts for equilibration # # ti_equil: Request generation of scripts for TI equilibration input # ti_equil_template: Template file for equilibration part of equilibration # phase of TI simulations. This equilibration part is # followed per default by a 1 ns free TI MD simulation # for complete equilibration of the system. # ti_equil_batch_template: Batch template file for equilibration phase of # TI simulations. # ti_equil_lambda: Values of lambda that shall be used in the calculation # in ascending order. Please specify only the decimal digits, # e.g. 1 for lambda 0.1, 05 for lambda 0.05. ti_equil 0 ti_equil_template /home/user/tutorial/input_info/equi_noShake_TI.in ti_equil_batch_template /home/user/tutorial/input_info/equi_TI.sge ti_equil_lambda 1,2,3,4,5,6,7,8,9 # # B) Setup scripts for production # # ATTENTION: This setup step can only be conducted if the equilibration # calculations have been completed. # # ti_production: Request generation of scripts for TI production input. # This setup step requires that the equilibration output is # present in the corresponding 'equi' folder. # ti_prod_lambda: Lambda steps for which the production shall be run; # separated by comma and in ascending order. Please specify # only the decimal digits, e.g. 1 for lambda 0.1. # total_ti_prod_time: Total production time requested (in ns) # ti_prod_batch_template: Batch template for TI production simulations # converge_check_script: Location of perl program to be used for convergence # checking after each production step. If the location # is not specified, it will be assumed that the program # can be found under the default location # at .../FEW/miscellaneous/convergenceCheck.pl # converge_check_method: Method that shall be used for convergence checking. # 1: Difference in standard error of dV/dL # 2: Precision of dV/dL according to student's # distribution # converge_error_limit: Error limit that shall be used as termination criterion # for the TI production simulations. # Defaults: 0.01 kcal/mol for method 1 # 0.2 kcal/mol for method 2 ti_production 0 ti_prod_lambda 1,2,3,4,5,6,7,8,9 total_ti_prod_time 1,1,1,1,1,1,1,1,1 ti_prod_batch_template /home/user/tutorial/input_info/prod_TI.sge converge_check_script converge_check_method 2 converge_error_limit 0.2