It's a little unclear to me exactly what went wrong. No code in Chimera issues a message containing the phrase "poor connection". Perhaps you could send me a session of your structure just after you make the serine/uracil bond and then I can run it myself through Dock Prep and get a better understanding of the problem.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On May 13, 2021, at 9:38 PM, Zhang, Bixia <bixia.zhang@wsu.edu> wrote:

Good evening,
I was trying to make a man made side chain, which is serine plus uracil. I used the command “bond sel” to connect the oxygen and nitrogen. Then I was trying to do docking to see if this mutation changed the binding affinity. However, after I ran dock prep, the uracil was got rid of because of “poor connection”. I am wondering if this arbitrary bond is feasible in chimera and can I do docking with this artificial model?
Thank you,
Bixia
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