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° | pKaRes | - | Set/get residue pKa |
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| | | Command | | Argument | | Datatype | | Default | | Min | | Max | |
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| Format: | | pKaRes | Residue selection, | | SELECTION | | - | | - | | - | | |
| | value = new residue pKa value | | FLOAT | | - | | - | | - | | |||
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| Python: | | pKaRes(selection1,value) resultlist = pKaRes(selection1) | |
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| Menu: | | Options > Residue pKa | | ||||||||||
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| Related: | | pH |
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| Required: | |
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The pKaRes command sets or gets the pKas of the selected residues.
The pKas set by pKaRes
replace those predicted by YASARA during the neutralization experiment
. When pKas of important (active site) residues have been measured experimentally,
it is recommended to specify them with pKaRes
before setting up a simulation. This ensures that the protonation states assigned by YASARA correctly reflect the chosen
pH.
When no new pKa is set,
the pKaRes command returns the currently set pKa or
-1 of no pKa has been assigned to a given residue before. pKaRes
does not predict pKa values by itself.
The pKa assignments are properties attached to the first atom in a residue,
hence they are saved with SaveSce and SaveYOb.
Example 1:
pKaRes His 70,value=2.5
Set the pKa of residue His 70 to 2.5 and consider this value during the next neutralization
experiment.
Example 2:
pKaRes Obj 5,value=None
Delete all pKa assignments in object 5.
Example 3:
pka = pKaRes Asp 80
Get the previously set pKa value of residue Asp 80 and assign it to variable
'pka'.