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Confusing trivalent sulfur that shouldn't get a generic but does #40
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And again, the smirks patter @davidlmobley |
When the same molecule as above gets charged, it becomes a sulfur with a negative charge: Is it possible the forcefield module is interpreting it as having a -1 charge to begin with? I'm going to try removing the +0 from that torsion and see if anything changes. |
It seems that all of them with this set in the tripos mol2 files don't get a generic if I fix the SMIRKS so it is
This is the same fix we used for the relevant bonds, as in smarty issue#216 |
Added |
I initially thought this molecule was only in the unfiltered DrugBank, but we do have a Tripos mol2 file for it (no gaff2 mol2 file). The highlighted torsion is assigned the generic, which doesn't make sense to me as there is a SMIRKS pattern in the smirffishfrcmod file that matches it.
This image is a little confusing because in 2D there are 2 oxygens overlapping only the black one is bound to the sulfur. The highlight torsion should match this line from smirffishFrcmod:
[*:1]~[#16X4,#16X3+0:2]-[#6X4:3]-[*:4] 1 0.000 0.0 3 Frosst X_-SO-CT-X guess
The highlighted torsion does match the smirks pattern if I load it into the substrucDepict notebook so I'm unsure why it is being assigned incorrectly.
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