Re: [AMBER] Error in Running tLEaP for Protein File

From: David A Case <>
Date: Mon, 22 Oct 2018 14:55:09 -0400

On Tue, Oct 23, 2018, Amartya Pradhan wrote:
> While running tLEaP for the protein file, I m getting the following error:
> >Created a new atom named: HD1 within residue: .R<HIE 24>

This error is because you have an HD1 atom in the PDB file, which should
not be there if the residue is indeed HIE (or HIS, which defaults to
HIE). You need to edit the PDB file to specify how you want this
histidine to be protonated.

> >Created a new atom named: HN1 within residue: .R<LIG 219>
> >Created a new atom named: HN2 within residue: .R<LIG 219>
> >Created a new atom named: HC23 within residue: .R<LIG 219>
> >Created a new atom named: HC24 within residue: .R<LIG 219>

This is a different error: your PDB file has the atoms named above in
the LIG residue, but the library file (probably loaded by means of a
.mol2 or a .off file) doesn't have those hydrogen names. Again, you
need to edit the PDB file to make the names of the hydrogens match those
in the library file.

I'll take this opportunity to remind people that tleap is at heart just a
bookkeeping program: it doesn't know anything about chemistry or
biochemistry: it is just trying to match up every atom in the input PDB
file to the appropriate atom in the library files that have been loaded.

If you get a "Created new atom" message, that means there is an atom in
the PDB file that is not in the library.

...good luck...dac

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Received on Mon Oct 22 2018 - 12:00:03 PDT
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