Hello Amber users,
Happy New Year to all of you.
I tried to generate topology and coordinate files for my ligand-protein
complex following tutorial
https://ambermd.org/tutorials/basic/tutorial4b/index.php. After I ran
tleap, in the new pdb, all the C=O bonds of amides in my ligand became
single bonds, but no charge or hydrogen was added to carbon or oxygen
atoms. Does anyone have ideas what happened? Thank you.
Kind regards,
Zeyu
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Received on Sat Jan 04 2025 - 10:30:02 PST
