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CVB¶
`MOZYME <mozyme.html>`__ calculation, a Lewis
structure cannot be constructed from the topology of the system
supplied. When that happens, a warning message will be printed and
the run stopped. Unwanted connections can be removed using CVB.
Two formats are supported:CVB(n1:-n2[;n3:-n4[;n5:-n6....]]])
where the connections to be removed are those between atoms n1-n2,
n3-n4, n5-n6, etc. See atom numbering. Thus if
connections were to be removed between atoms 4 and 5, and between atoms
665 and 670, then CVB(4:-5;665:-670) would be used. If connections
are needed, then don’t use the minus sign. Thus if connections were
needed between atoms 4 and 5, and between atoms 665 and 670, then
CVB(4:5,665:670) would be used. CVB is also useful when
`RESIDUES <residues.html>`__ and PDBOUT are present. A topology
sometimes has an unwanted connection between two chains that prevents
some of the residues being identified. To correct this fault, remove
the unwanted connection using CVB. If there are a several unwanted
connections , and these connections involve a specific element, then
consider the alternative of using VDWM to change the Van der Waals
radius for that element.
Using atom labels
CVB("Label1":-"Label2"[;"Label3":-"Label4"[;"Label5":-"Label6"....]]])
Here Labeln is the label, in PDB or JSmol format, for the atom.
Using the PDB format, the label starts with the first non-blank
character of the atom name and ends with the last character of the
residue number. For example:
CVB("2HB SER B 4":-"OD1 ASP B 119","1HH1 ARG B 5":"C TYR B 7").
Spaces are not important, but using spaces makes it easier to read the
atom label. With JSmol, the label starts with a “[” and ends at the
character before ” #”. As with PDB format, spaces are not important
when JSmol format is used, i.e.,
CVB("[LYS] 4 : A . CD":"[LYS]4:A.CG"). The advantage of using
atom labels is that if atoms are added or removed the atom label would
not change. Another advantage is that PDB TER lines, positional
disorder, and other things that cause the PDB line number to not match
the atom number do not cause problems.
Wildcards are allowed for the residue name and for the chain letter.
When a wildcard is used, a letter is replaced by an asterisk, “*”,
thus:CVB("2HB *** B 4":-"OD1 *** * 119","1HH1 ARG * 5":"C TYR B 7")andCVB("[***] 4 : * . CD":"[***]4:*.CG").
The first occurrence that matches will be used.
Special case of O-O bonds.¶
When proteins that contain a large number of water molecules are edited, quite often one or more water molecules become badly positioned, resulting in spurious O-O interactions. These can be eliminated using the standard options within the CVB keyword, but as this problem occurs quite often, a special option, “O:-O” is provided. This six-character option will identify and delete all spurious O-O bonds.The option can be anywhere between the opening “(” and closing “)” of the CVB keyword.
Intermediates in Enzyme Mechanisms¶
A frequent problem when modeling intermediates and transition
states in enzyme mechanisms is that the structure cannot be written in
Lewis form. An example occurs in the transition state when a cystine
sulfur starts to bond to the carbon of a guanidinium group in an Arg,
and the hydrogen that was on the sulfur migrates to one of the nitrogen
atoms of the guanidinium. If this happens, the resulting -NH:sub:3
group would have a positive charge and the carbon would be given a
negative charge. (A carbon atom bonded to a cation and having only
three valencies used would automatically be assigned a negative charge.)
Sulfur having only one bond (to its CH2 group) is, by default,
also given a negative charge. The net charge on this assembly is now -1
instead of the expected +1. To correct this error CVB is used to
make a bond between S and the H of -NH:sub:3. This automatically
causes the N-H bond to be deleted giving -NH:sub:2, a component of the
normal guanidinium group. Now that sulfur is bonded to its hydrogen as
will as to its CH2 group, and the guanidinium has the usual +1
charge, the net charge in this region is correct.
A guiding principle would be to use CVB to make the structure as
similar to either the reactant or product as possible.
Note that CVB is used only in the generation of a starting Lewis
structure or in generating a PDB file. The presence of unrealistic
connections in this structure will not normally give rise to an
incorrect SCF.
See also SETPI to explicitly assign π bonds, and atom
labels to explicitly assign charges.
Related keywords:
++, SETPI, LEWIS, CHARGES, METAL, VDWM, CHARGE, XENO, and MOZYME