On Sun, Aug 30, 2020, Kashyap, Jatin wrote:
>
>I used UCSF chimera to add hydrogen & charge and saved the result in pdb
>format and fed to AMBER. Here one thing to notice, I do get some alerts in
>UCSF chimera while adding charge.
Charges are not generally stored in PDB files, and Amber doesn't read
such information from there. If you are preparing a ligand PDB file for
antechamber, use the '-nc' flag to set the net charge on the ligand.
And double-check that chimera is doing sensible things when adding
hydrogens.
...good luck....dac
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Received on Mon Aug 31 2020 - 05:30:03 PDT
