MacroModel Reference Manual - ISP

Appendix E: The BMFF Protocolforce-field file would be called f10.fld. Customers developing their own in-house applicationsare free to use values of 100 or greater for nn.The extended force-field file contains, on the first non-blank line, the word Process:,followed by a command line: typically, a process name plus (perhaps) command-line arguments.If the process name contains the character /, the named executable image is used; otherwise,the process with the given name is searched for first in the local directory and, if notfound, in the $SCHRODINGER/mmshare-vversion/data directory.Following the Process: line, there may be one or more Option: lines. These specifycommand-line options for the server process that the user can invoke by means of arg4 of theFFLD command. Each Option: line should include an integer followed by one or morestrings. If an integer given on an Option: line is specified in arg4 of FFLD, then the stringswill be appended to the command-line when the process is started. Right now, only a singleoption specified in this manner can be used at run-time. Both the Process: and the Option:lines use free format; their contents consist of strings separated by spaces, but no tabs areallowed.Beyond the first few lines, the extended force-field file follows the plan of a normal Macro-Model force-field file. The STR, BND, etc. keywords define the equations which MacroModel isto use internally to describe stretches, bends, etc. MacroModel will call on the server, eventually,to obtain the atoms constituting the interactions and the corresponding parameters. Forvan der Waals and hydrogen-bonding interactions, the constituent atoms are passed to theserver as needed, and the corresponding parameters are passed back whenever the pair-list isupdated. Universal constants associated with the various interaction equations are specified onthe equation lines for BMFF force-fields; see f10.fld for examples. In a BMFF force-fieldfile,The Main Interaction Section of the file may specify general interactions. If present, these willoverride the corresponding parameters obtained by the server. Similarly, the SubstructureSection may contain overriding parameters for molecular substructures. The substructuresection may also specify additional interactions (e.g., remote torsions) not created by the serverprocess. If overriding parameters or added interactions are actually used, a warning messagewill be printed to the MacroModel log file. The server process may also write to the commandfile simply by writing to the UNIX standard output.When the nonbonded pair list is updated, MacroModel (the client) passes each interactingatom-pair to the server and receives back the parameters for that pair; if overriding parametersexist for this pair, the server is not called. (If fast VDW processing is in effect, the client-sidelibrary stores a table of nonbonded parameters by pair type. In this situation, the server is nevercontacted for a nonbonded update. Here, this table is not consulted if overriding parametersexist for the pair in question.)222MacroModel 9.7 Reference Manual