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Chapter 17. "Types" of metal cation

17.1. Metal cation probes

17.1.1. Type 110 (JTYPE = 110)

This Type is the default value (JTYPE=110) for metal cation Probes. These Probes must be assigned appropriate Van der Waals parameters, and must have a positive charge because they are cations. They must not be assigned any hydrogen bonding variables because metal cations do not make hydrogen bonds.

In early releases of the Programmes a metal cation Probe was just be regarded as a charge with a Van der Waals radius and a polarizability. It was assigned the value JTYPE=0 and its electrostatic interactions with other atoms were computed as isotropic interaction energies between point charges.

In this release of the Programmes the lone pair orientations of the Target atoms will be taken into account when the cationic metal Probe has a JTYPE value in the range 110 to 114 inclusive. For example, a calcium ion with JTYPE=110 will tend to interact most favourably with a carboxyl oxygen atom of the Target when it is in the plane of the carboxyl group.

Therefore, by default, cationic metal Probes should always be assigned the value JTYPE=110. This would be the default value to use if you wanted to devise new energy variables for a new metal cation. In most cases, however, better results can be attained by using one of the following JTYPE values (111-114).

Type 110 should not be used for cations in the Target.

Note on JTYPE for metal cation probes: Metal cations do not make hydrogen bonds, but the variable JTYPE is used nevertheless in order to define their properties. This is a special use of JTYPE.

17.1.2. Type 111 (JTYPE = 111)

This Type (JTYPE=111) specifies cationic metal Probes which interact in a particularly favourable way with oxygen ligands. The specificity of the interaction is determined by the chemical hardness of the Probe cation. Such Probes will also interact favourably with nitrogen, but do not accept sulphur ligands so readily. These Probes must be assigned appropriate Van der Waals parameters, and must have a positive charge because they are cations. They must not have any hydrogen bonding variables because metal cations do not make hydrogen bonds. Typical Probes which should be assigned the value JTYPE=111 include:

LI+  NA+  K+  CA+2 SC+3 RB+  SR+2 CS+  BA+2

Other Probes which might be assigned this value would be:

MG+2  V+3  CR+2  CR+3  MN+2

but it would usually be more appropriate to assign JTYPE=112 to the list of Probes from MG+2 to MN+2.

Type 111 should not be used for cations in the Target.

17.1.3. Type 112 (JTYPE = 112)

This Type (JTYPE=112) specifies cationic metal Probes which interact in a particularly favourable way with nitrogen or oxygen ligands. The specificity of the interaction is determined by the chemical hardness or softness of the Probe cation. Such Probes will not accept sulphur ligands so readily as oxygen and nitrogen.

These Probes must be assigned appropriate Van der Waals parameters, and must have a positive charge because they are cations. They must not have any hydrogen bonding variables because metal cations do not make hydrogen bonds.

Typical Probes which should be assigned the value JTYPE=112 include:

MG+2 V+3 CR+2 CR+3 MN+2

Type 112 should not be used for cations in the Target.

17.1.4. Type 113 (JTYPE = 113)

This Type (JTYPE=113) specifies cationic metal Probes which interact in a particularly favourable way with nitrogen ligands. The specificity of the interaction is determined by the chemical hardness or softness of the Probe cation. Such Probes may also interact with sulphur, but do not accept oxygen ligands so readily.

Typical Probes which should be assigned the value JTYPE=113 include:

FE+2 FE+3 CO+2 CO+3 NI+2 CU+2 ZN+2 and perhaps CU+

Type 113 should not be used for cations in the Target.

17.1.5. Type 114 (JTYPE = 114)

This Type (JTYPE=114) specifies cationic metal Probes which interact in a particularly favourable way with sulphur ligands. The specificity of the interaction is determined by the chemical hardness or softness of the Probe cation. Such Probes will also interact with nitrogen, but do not accept sulphur ligands so readily.

CU+ is a typical Probe which should be assigned the value JTYPE=114

Other Probes which might be assigned this value 114 would be:

FE+2 FE+3 CO+2 CO+3 NI+2 CU+2 ZN+2

However these Probes (from FE+2 to ZN+2) are normally assigned the value JTYPE=113

Type 114 should not be used for cations in the Target.

17.1.6. Type 115-119 (JTYPE =115-119)

These values are reserved for future use by Molecular Discovery. They should never be used for cations in the Target.

17.2. Metal cations of the target

Metal cations of the Target may be represented by HETATM records. Their energy variables are then taken form the last HET Section of Datafile GRUB, and they are assigned the value ITYPE=0 by default. Cations with this value of ITYPE are fixed in the Target at the position specified by their coordinates in the PDB input file, and this is what one usually wants. For instance the manganese in superoxide dismutase is in a fixed position.

Certain metal cations are normally represented by ATOM records. For example the HAEM entry in Datafile GRUB includes an ATOM record for iron, and this iron atom is also assigned as TYPE=0 which means that its position is fixed.

However, one may sometimes want to have counter-ions in solution round the main Target molecule. For instance a Target may appear to have an excess negative charge when its file is first extracted from the Brookhaven Data Bank, because it has excess of anionic (ASP, GLU) residues, and it may then be desirable to add appropriate counter-cations to the PDB file in order to reduce the overall charge. Such counter-ions may be assigned as TYPE 120 which allows them to move in response to the Probe when Directive MOVE ≠0 in Programme GRID.

Special ATOM entries for NA+ and K+ are provided in Datafile GRUB for this job. These ATOM entries are completely distinct from the HETATM entries for sodium and potassium in the HET Section at the end of Datafile GRUB. The ATOM entries NA+ and/or K+ are explicitly for use as counter-cations. An ATOM entry for chloride CL- as a counter-anion is also provided, in case the Target has a net positive charge due to excess cationic (ARG, LYS, HIS) residues.

Directive MOVE with counter-ions: Type 120 counter-ions do not move in response to the Probe when MOVE=0 in Programme GRID. They move and flexible Target atoms also move when MOVE>0. Type 120 counter-ions move but flexible Target atoms do not move when MOVE=-1

Note on molecule names for counter-ions: When the special ATOM entries NA+ K+ and CL- are used, each ion must have the correct molecule name (variable ACID) in the PDB file. These molecule names are SOD, POT and CHL respectively as shown in GRUB.

The ATOM records for NA+ K+ and Cl- are assigned to Type 120 (ie: they have ITYPE=120) in Datafile GRUB, and this special Type is also automatically assigned by Programme GRIN to the potassium and magnesium counter-ions of DNA Targets. Type 120 counter-ions have the following properties:

17.2.1. Type 120 (ITYPE = 120)

Type 120 is normally used for the counter-ions of a protein Target. It will also be assigned automatically by Programme GRIN to the potassium and/or magnesium counter-ions of DNA Targets, and it may be used for chloride as a counter-anion on a protein Target. In each of these cases the TYPE 120 counter ion should be an ATOM record of the PDB input file.

Note that the Symbol ITYPE is used instead of JTYPE, in order to emphasise that ITYPE=120 is the assignment for a Target atom and not for a Probe. This special assignment ITYPE=120 has the following effects:

The ordinary default value ITYPE=0 is assigned from Datafile GRUB to any counter-ions which are represented in the Target by HETATM records. (It is of course necessary to set Directive NETA in Programme GRID, so that these HETATMs will be included as a part of the Target).
Type 120 counter-ions of the Target should normally be ATOM records. Their properties are defined in the main Section of Datafile GRUB. This Datafile is supplied by Molecular Discovery Limited with ATOM records for the counter-ions NA+ K+ and CL-. Of course the User may add other ITYPE=120 counter-ions to his or her copy of GRUB.
An assignment to ITYPE=120 is also made for the counter-ions of DNA (and RNA) Targets when ATOM records are used for the DNA (or RNA). In this case each phosphate group of the DNA (or RNA) normally gets one potassium counter-ion. However a pair of TYPE 120 potassium counter-cations on DNA may sometimes be replaced by a single Magnesium ion.
TYPE 120 counter-ions of the Target behave normally if directive MOVE=0 in the main Programme GRID. Their position in the Target is then fixed.
TYPE 120 counter-ions of the Target can move in response to the Probe when directive MOVE>0 in the main Programme GRID. They may attract or repel the Probe (depending on their distance and charge), or may be pushed away by a Probe which gets too close. Flexible Target atoms also move in response to the probe when MOVE>0
TYPE 120 counter-ions of the Target also move in response to the Probe when directive MOVE=-1 in the main Programme GRID, but flexible Target atoms do not move in this case.
The algorithms in this Version of the Programme cannot deal with a close cluster of TYPE 120 counter-ions, and we therefore recommend a separation of at least 6 Angstrom between each TYPE 120 counter-ion and its nearest Type 120 neighbour in the Target.
When a multi-atom Probe is being used, a wider spacing of at least 8 Angstrom between TYPE 120 counter-ions is recommended.
The User may substitute the default value (ITYPE=0) instead of the special assignment ITYPE=120 for any counter-ion of the Target. This substitution may be made in Datafile GRUB, or in the GRINKOUT file for one particular Target.
The User may alternatively substitute the special value (ITYPE=120) instead of the default assignment ITYPE=0 for any counter-ion of the Target. This substitution may be made in Datafile GRUB, or in the GRINKOUT file for one particular Target. Particular care is needed when ions are given the value ITYPE=120 by the User.
Type 120 may not be used for Probes.

Further information is provided below under the Heading: NUCLEIC ACID COUNTER IONS. This should be carefully studied by Users who want to assign ITYPE=120 themselves.

17.3. Chloride counter-anions

Counter anions may be added to the PDB file for a protein, or to the file of any other biological macro-molecule, in order to compensate for an excessive positive charge of the Target. These counter-anions may be defined by regular HETATM records (with ITYPE=0), or as ATOM records for chloride Any ATOM records for chloride counter-ions will be assigned by Datafile GRUB as ITYPE=120 counter-ions.

TYPE 120 chloride counter-anions have similar properties to Type 120 metal cations. They can move in response to the Probe when Directive MOVE≠0 in Programme GRID. See above (under METAL CATIONS OF THE TARGET), and below under NUCLEIC ACID COUNTER IONS for more information about the treatment of TYPE 120 counter-ions.

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