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CHARMM DNA patches have a missing bond #341

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iwan-grin opened this issue Jul 1, 2024 · 0 comments
Open

CHARMM DNA patches have a missing bond #341

iwan-grin opened this issue Jul 1, 2024 · 0 comments

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@iwan-grin
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Greetings all.

It seems to me that the DEO5 and DEOX patches in charmm36.xml are slightly wrong. Both of them remove the O2' from nucleotides to make them desoxynucleotides. However, they fail to introduce a bond between C2' and H2', leaving the H2' floating in space.

Proposed fix:

<AddBond atomName1="C2'" atomName2="H2'"/>
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