CHARMM Element doc/mmff.doc 1.1#File: MMFF, Node: Top, Up: (chmdoc/commands.doc), Next: Usage Merck Molecular Force Field (MMFF94)* Menu:* Usage:: How to use MMFF with CHARMM standalone* Quanta:: How to use MMFF from QUANTA* Status:: Current status of MMFF implementation in CHARMM* Theory:: Basis for, parameterization and performance of MMFF94* Funcform:: Functional form of the MMFF energy expression* Refs:: References to papers describing MMFF94* Parameters:(chmdoc/mmff_params.doc). MMFF Parameters#File: MMFF, Node: Usage, Up: Top, Next: Quanta, Previous: TopIn order to use MMFF in CHARMM, the user has to issue the followingcommands:1. use mmff force field2. <read mmff parameter files>3. (a) read rtf name <MMFF-capable rtf file>, or (b) read merck name <file_name> (c) read mol2 name <file_name> (d) read db mol_name name <file_name>4. read sequence ! if input is via the rtf route (step 3 (a))5. generate ! note that there may be multiple segments in one .mrk file6. patch ! if input is via rtf/sequence route, apply appropriate patches ! to force a new mmff_setup; either include the keyword "mmff" ! on the final patch or follow the final patch by the command: ! "use mmff atom types"7. read coord, or ic build ! if input is via the read rtf/sequence route. Steps 1 & 2 can be done by streaming the file "mmff_setup.STR." An exampleof this file is shown below. Documantation on the contents and usage of theMMFF parameter files may be found in mmff_params.doc.Step 3a requires a MMFF-capable rtf file. This means a file in which BOND records have been replaced by analogous DOUBLE or TRIPLE records forcases in which the chemical structure (or any valid Kekule representation)has a double or triple bond. Mass records in a MMFF-capable rtf file must also be augmented to add the atomic symbol for each CHARMM atom typeafter the atomic mass entry. Note that MMFF-capable rtf files are *back compatible*. That is, such rtf files can equally well be used for calculations that utilize the CHARMM force field. Thus, it is *not* necessary to maintain two versions of the rtf files.Format of .mrk file optionally read in step 3b----------------------------------------------Merck-format files consist of one or more consecutive molecular-data entries.Note: when embedded in a CHARMM input script, a mrk file must be followed bya card reading "END" in columns 1:3.FILE_FORMAT:All entries in a Merck-format (.mrk) file have the format: Line # # of Lines Use1 1 Header_1 2 1 Header_2 3 1 Number of atoms and bonds 4 n Data on n atoms 4+n k Bonding data on the 5*k bonds in the structure (Each line contains data on five bonds) Header_1:The format for the first header line is:(A70,A10)Each field contains the following information: column Description of use 1-70 User defined title 71-72 Present Year (YY) 73-75 Present Date (DDD) 76-79 Time of Day (HHMM), e.g., "1709" for 5:09 pm 80 Must be a "1" for the file to be valid Header_2:The second header line has the following format:(A4,A8,X,A1,X,A65)Each of the fields has the following information: column Description of use 1- 4 The string "MOL " 5-12 User name 14 Source of file : (e.g., E for MOLEDIT, C for Cambridge, D for Distance Geometry etc.) 16-80 Column used by other programs such as the Cambridge Programs and OPTIMOL Number_of_atoms_and_bonds:The format for this record is:(I5,X,I5)Each of the fields has the following information: column Description of use 1-5 NATOM 7-11 NBND Data_on_atom_n:The format for the atom records is: (3(F10.4,1X),I5,1X,I2,1X,I1,1X,I5,1X,3A4,F8.4,6X,A4)Each of the fields has the following information: Columns Field Description1-10 X X coordinate of the atom 12-21 Y Y coordinate of the atom 23-32 Z Z coordinate of the atom 34-38 Atomic Number (I5) field containing the type of atom. (i.e. -- 6 for Carbon; 8 for Oxygen; etc...) A value of 0 indicates a lone pair. 40-41 Atom Subtype (I2) field: on output, contains the MMFF atom type; is not read on input 43 Charge Code Formal charge code of the atom. 45-49 Sequence Number (I5) field containing the unique number by which every atom in the structure can be identified. Note: in the CHARMM implementation, these quantities are not actually read. However, the atoms are expected to be numbered consecutively from 1 to NATOM and to correspond to the numbers used in the bond_data records defined below. 51-54 Atom Name Left justified (A4) field. Should be unique inside a given residue. (Examples -- "C24 ", "NH ", etc...). 55-58 Residue Name Right justified (A4) field. (Examples -- " 123", "123A", etc...). 59-62 Residue Type Left justified (A4) field. (Examples -- "TRP ", "LYS ", etc...). 63-70 Partial Charge (F8.4) field containing the partial charge of an