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

From: Kashyap, Jatin <>
Date: Sun, 30 Aug 2020 00:45:39 -0400

Hi David,

Thanks for response. Actually, it's a acid/protein complex 2nnq. I am
removing the water, ions from complex and separating them using pymol. Then
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.

On Sat, Aug 29, 2020, 1:24 PM David A Case <> wrote:

> 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
> >version.
> 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?
> ....dac
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Received on Sat Aug 29 2020 - 22:00:02 PDT
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