On Sat, Jan 04, 2025, Zeyu Lin via AMBER wrote:
>
>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.
Neither PDB files, nor Amber force fields, know anything about whether bonds
are "single" or "double".
I suspect(?) that the reason you think the C--O bonds in your ligand are
"single" has to do with whatever visualization program you are using to look
at the PDB file.
(It this doesn't solve your problem, we would need to know more about
exactly what makes you conclude that the bonds are single.)
...dac
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Received on Sat Jan 04 2025 - 10:30:02 PST
