Change order to appropriately type Carboxylates
Closed this issue · 5 comments
I realized this while I was looking at the which carbonyl option should be used for the more generic carbon option. There is a bond for "carboxylates" C(=O)[O-] groups such as this molecule:
I would assume that the two oxygens in a carboxylate should be treated equally (like a nitrogroup) since there are equal resonance structures for the two oxygens. However the carbon with the negative charge gets this bond:
[#6X3:1](~[#8X1])~[#8X1:2] 656.0 1.250 parm99 carboxylate C~O
And the other oxygen (drawn with the double bond) gets the carbonyl assignment:
[#6X3:1]=[#8X1+0,#8X2+1:2] 570.0 1.229 parm99 carbonyl oxygen
In the smirffish file that is the order these appear in, I don't yet have a suggestion on how to fix this assuming they are supposed to be assigned the same parameter.
@davidlmobley ( @cbayly13 we may need you on this one)
I think if we switch the order so
[#6X3:1]=[#8X1+0,#8X2+1:2] 570.0 1.229 parm99 carbonyl oxygen
[#6X3:1](~[#8X1])~[#8X1:2] 656.0 1.250 parm99 carboxylate C~O
It should fix the problem... I'm trying to think of any situations where this wouldn't work.
@bannanc - do you have a charged mol2 for these you can peer at? If the oxygens are getting hte same charge (which I would guess they are) then I would agree with you that the bonds ought to have the same parameters.
@bannanc is correct, we just need to switch the order like she says. The
[#6X3:1](~[#8X1])~[#8X1:2] 656.0 1.250 parm99 carboxylate C~O
parameter will only be applied to carboxylates (or carbonates or carbamates) and the tildes are good generality to accommodate the different ways carboxylate can be written.