Unique Input Statements
CONTACT <Type> <Type> <Distance> <Standard deviation>
The CONTACT statement defines the allowed contact distances for non-bonded contacts between atoms. Contacts between non-bonded atoms are screened every time the other geometry restraints are checked, and if two non-bonded atoms are closer than the minimum contact distance they will be flagged as a bad contact and will be pushed apart by refinement. Whether two atoms are bonded is determined by checking the list of standard bond lengths. All 1-2, 1-3, and 1-4 contacts are ignored. These kinds of interactions are covered in bond length, bond angle, and torsion angle refinement, respectively, and should not be considered again.
The information that should be placed on this statement is the elemental types of the two elements, the minimum contact distance, and the individual standard deviation for that particular contact, in the following form:
CONTACT O C 2.8 0.1
This means that the minimum non-bonded contact distance allowed between an atom of carbon and an atom of oxygen is 2.8Å with a sigma of 0.1Å. (Note: This restraint is based only on the type of the atoms involved where the other kinds of restraints depend on the name of the atom and the residue type.)
A library of CONTACT statements for many atom types is provided in the file $tntdata/contact.dat (in TNT_DATA:CONTACT.DAT on VMS). A description of the sources of information used to generate these values is contained within this file.
It is quite difficult to find a proper set of values for the closest allowed distances between to element types. The values in contact.dat have been purposely chosen to be small. This ensures that a contact flagged ``bad'' will really be bad. However there are some cases where the local chemistry allows two atoms to approach one another so closely the the library defines a contact as ``bad'' when it really is not. These particular cases should be EXCLUDEd.
EXCLUDE [<Chain>|]<Residue>[:<Atom>] -
[<Chain>|]<Residue>[:<Atom>]
This statement causes any close contacts between atoms in one group with any atom in the other group to be ignored when deciding what the bad contacts are. A group is defined by giving the chain name, residue name, and atom name of the atom whose contacts are to be ignored. Wild card may be placed in any position. The default residue and atom names are wild cards, but the default chain name is the ``chain with no name''. To specify an entire residue one gives the residue name. To specify a particular atom one gives the residue name and the atom name separated by a colon. To specify all atoms with the same name leave the residue name blank and provide a wild card (``*'') as the chain name. Here are some examples.
In the first example all contacts between any atoms in residue 143 with atoms in residue 167 will be ignored. The second example states that if a bad contact is found to exist between atom O of residue 67 and atom O65 of residue SOL1 that contact will be ignored. In the third example the program will ignore all contacts between atoms named O and atoms named C anywhere in the structure.
Here is an example of a use of the EXCLUDE statement which uses the oligomer definition of Cro given as an example in the ``TNT Sequence File'' chapter of the TNT Users' Guide.
EXCLUDE O| O|
EXCLUDE A| A|
EXCLUDE B| B|
EXCLUDE C| C|
These EXCLUDE statements will cause all non-bonded contacts within CRO chains to be ignored leaving only interchain contacts to be listed and refined.
WEIGHT BOND <x> TORSION <x> PLANE <x> PSEUDO <x> WEIGHT ANGLE <x> TRIGONAL <x> BCORREL <x> CONTACT <x>
This statement is used to specify the weights to be applied to each class of stereochemical restraint. Each name of a restraint type is followed by the weight that type is to be given. Chiral centers cannot be refined and therefore there is no way to define a weight for that class of restraints (If you want to call something that cannot be refined a restraint).
There is a great deal of flexibility in the arrangement of the weight definitions. The weights can be defined in any order, and can be placed on several different WEIGHT statements. Geometry will ignore weights from other modules.