Re: [AMBER] "FATAL: Atom *** does not have a type" Error

From: David A Case <>
Date: Sat, 29 Aug 2020 13:23:59 -0400

On Sat, Aug 29, 2020, Jatin Kashyap wrote:
>I am trying to perform MD run on a ligand-receptor complex after
>splitting and preparing them individually in PyMol from a RCSB downloaded

I'm not sure what you/PyMol did, but it looks like there are problems
with your PDB file:

>Created a new atom named: HA2 within residue: .R<GLU 54>
>Created a new atom named: HA3 within residue: .R<GLU 54>

This says that atoms with the above name are in the PDB file, but GLU
would never have such atoms.

>Created a new atom named: HG1 within residue: .R<LYS 79>

Same type of problem: LYS doesn't have an HG1 atom.

You can strip all the hydrogens and try again, but I fear that other
problems (missing atoms) may have crept in as well. Why do you need
PyMol in this workflow?


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Received on Sat Aug 29 2020 - 10:30:02 PDT
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