[Chimera-users] Covalent bond making and docking

Zhang, Bixia bixia.zhang at wsu.edu
Thu May 13 21:38:11 PDT 2021

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,
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