Hi all,
I have a bizarre historical domain type of question about how the terminal atoms in ff86 get linked onto nucleosides.
So in ff86, the terminal H5'/H3' and the phosphate backbone (HB,HE, and DPOM) are all denoted as separate residues from the backbone/base/sugar, instead of keeping them all as a single merged nucleoside/nucleotide entry as in ol15. Given that, how does one add on the hydrogen/phosphate groups to the truncated nucleoside since it doesn't auto-add them natively? I played around with it but only arrived at two workarounds
1. Have a structure already with the hydrogen/phosphate present by manually 'guessing' where they should be
2. Rename the terminal O5'/O3' as residues DOHE so leap will add on the hydrogens, and delete the extra O3/O5 after
But I figured there should be a better way to add and link on terminal groups if I'm starting from just a 'truncated' nucleoside?
(I also realize the easy solution would be just to take a complete nucleoside/nucleotide from another source, rename the atoms and feed it into ff86, but I'm stuck with trying to do this internally within only ff86)
Best,
Kenneth
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Received on Thu Jan 20 2022 - 11:30:02 PST
