Re: [AMBER] LEaP Error/questions.

From: David A Case <>
Date: Tue, 12 Jan 2021 08:17:15 -0500

On Mon, Jan 11, 2021, Sam Walsworth (Researcher) wrote:
>Thank you for the help. I've come to realise when I swapped HIS to HIE to
>match residue names I was getting a single hydrogen that didn't match HIE
>lib file and did match HID. When I changed HIE to HID in the PDB file I was
>now getting other hydrogens, one per residue/multiple residues, that didn't
>match the HID lib file. I'm now working on the assumption that my enzyme
>has histidines both HID and HIE.

If you already have hydrogens in your input file, run through pdb4amber
first: it will decide what protonation state is there, and will adjust the
names accordingly.


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Received on Tue Jan 12 2021 - 05:30:03 PST
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