| CFF |
The CFF forcefield is accessed by selecting the Forcefield/Assign_CFF menu item of the Insight program's Builder module.
Pulldowns
Options in the Assign_CFF parameter block
Potential_Action
The Potential_Action control indicates what action is to be taken for the potentials of the model. Fix is used for changing to CFF potentials. Accept sets the potentials_ok flag of the model and may be used only when the CFF potentials are already set (as when .car and .mdf files produced with CFF are read in).
Partial_Chg_Action
The Partial_Chg_Action control indicates what action is to be taken for the partial charges of the model. Fix is used for changing to CFF charges. Accept sets the charges_ok flag of the model and may be used only when the CFF partial charges are already set.
Formal_Chg_Action
The Formal_Chg_Action control indicates what action is to be taken for the formal charges of the model. Accept is compatible with CFF. Fix recalculates the formal charges of the model.
Assembly/Mol_Name
The Assembly/Mol_Name control specifies the name of a model on which the command is to act.
Models are read into the Insight II interface from existing files using the Molecule/Get menu item or are constructed by using the sketcher. You can associating objects into assemblies, if desired, with the Associate command of the Assembly module. The Assign_CFF command functions with both molecules and assemblies.
Defining and entering a model
Charges and atom types for CFF are assigned when the Fix, Fix, and Accept parameters are selected for a model. After command execution, the CFF forcefield is selected and charges and atom types are assigned.
Charge and atom type assignments
Checking for undefined parameters and atom types
After execution of the Forcefield/Assign_CFF command it is best to look at the textport to see if any warning messages have appeared. Below are some examples of where this may occur.
(Executing: Assign_CFF Fix Fix Accept CAJ4) atypq: bad atomic element number `106' Error, atypq program failedExample 2
Planar ring system not in database--Just a warning
(Executing: Assign_CFF Fix Fix Accept PHDA) atypq: molecule 1: one or more ring systems in molecule not obtained from charge database -- substituting less accurate bond increment methodExample 3
Five hydrogens on methane?
(Executing: Assign_CFF Fix Fix Accept METC) atypq: WARNING: new atom types generated ( H ), check topologyExample 4
Missing bond increment parameters
(Executing: Assign_CFF Fix Fix Accept MPS) atypq: missing bond increment for si,osh, zero used atypq: missing bond increment for osh,hos, zero used
Other potential types of errors/problems/limitations
When CFF is properly installed, the only types of problems expected are those described above. If there are changes to the environment or path or if installation has failed, other messages can appear. While it is unlikely such errors ever occur, examples with solutions are given below.
(Executing: Assign_CFF Fix Fix Accept PHDA)output:
ezio lib: cannot open "/net/iris78/usr/people/wty/ BIOSYM_LIBRARY.ind": No such file or directory Error, atypq program faileddiagnoses:
$ATYPQARGS incorrectly set to $BIOSYM_LIBRARY, should be:remedy:
setenv ATYPQARGS -I$BIOSYM_LIBRARY/cff/cff_q:operation:
(Executing: Assign_CFF Fix Fix Accept MPS)output:
atypq: cannot find bond increment data-base Error, atypq program faileddiagnoses:
$ATYPQARGS incorrectly set to $BIOSYM_LIBRARY/cff, it should be:remedy:
setenv ATYPQARGS -I$BIOSYM_LIBRARY/cff/cff_q:operation:
(Executing: Assign_CFF Fix Fix Accept METC)output:
atypq: usage: atypq [-ceqdtPNhTArRz] [-iinputPrefix] [-i inputPrefix] [-ooutputPrefix] [-o outputPrefix] [-ffilePrefix] [-f filePrefix] [-mmodel.car] [- m model.car] [-Idbpath/prefix] [-I dbpath/prefix] equivAtyp ... Error, atypq program faileddiagnoses:
$ATYPQARGS contains additional arguments:operation:
(Executing: Assign_CFF Fix Fix Accept CAJ4)output:
atypq: usage: atypq [-ceqdtPrhTArR] [-iinputPrefix] [-i inputPrefix] [-ooutputPrefix] [-o outputPrefix] [-mmodel.car] [-m model.car] [-Idbpath/prefix] [-I dbpath/prefix] equivAtyp ... Error, atypq program faileddiagnoses:
Old format atypq program used (note missing z in argument list):operation:
(Executing: Assign_CFF Fix Fix Accept CRN)output:
Error, unable to open cff.frcdiagnoses:
The environmental variable ATYPQARGS is set incorrectly to "I_dont_know":operation:
(Executing: Assign_CFF Fix Fix Accept CRN)output:
Error, unable to open cff.frc (Repeat) User types control z to stop the process: Stopped iris152 lf $BIOSYM_LIBRARY/cff/cff_q.ind UX:ls: ERROR: Cannot access /ax10/bioroot/develop/ release960/irix5r3/biosym_lib//cff/cff_q.ind: No such file or directorydiagnoses:
Failure on install of cff/ directory, must reside in $BIOSYM_LIBRARY:operation:
(Executing: Assign_CFF Fix Fix Accept CRN)output:
process: "atypq -f/tmp/atypq12519": No such file or directory Command: User types control z to stop process: Stopped iris152 which atypq atypq not in . /usr/local2/ /net/iris78/usr/people/ wty/bin /usr/bsd /bin /usr/bin /usr/sbin /usr/etc / etc /usr/demos /usr/local/bin /usr/bin/X11 /polymer/ usr/local/bin /ax5/usr3/local/bin /usr/bin/dn /ax8/ local irix5r4 /ax10/bioroot/ccm/bin/irix5r4 /ax10/ bioroot/ccm/bin /ax8/local/bin /ax10/bioroot/develop/ release960/biosym_bin /ax10/bioroot/develop/ release960/irix5r3/biosym_exediagnoses:
path is not set to contain the $BIOSYM_LIBRARY/cff directory