Re: [AMBER] Missing atom types for ligand with chlorine atoms

From: David A Case <>
Date: Tue, 16 Mar 2021 09:03:08 -0400

On Tue, Mar 16, 2021, Aliakbartehrani Zahra wrote:

>FATAL: Atom .R<SDF 369>.A<CL72 72> does not have a type.
>FATAL: Atom .R<SDF 369>.A<CL82 73> does not have a type.

This error message means that there is an atom named "CL72" in residue 369
in your PDF file, but no atom named CL72 in the SDF unit you have defined.

>loadmol2 lig-WithH.mol2
>loadamberprep lig-WithH.prep
>loadoff lig-WithH.lib

This is very odd: you are loading three different versions of the lig-WithH
files. You only need one of these! I'd recommend just using the mol2 file,
since its format is very simple, and you can even edit it by hand if needed.
Check in lig-WithH.mol2 and see if the atom names match those in your PDB
file. You will probably need to hand-edit one or the other of these files
to make them match.

Atom names are indeed case-sensitive, but that may or may not be relevant here.


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Received on Tue Mar 16 2021 - 06:30:02 PDT
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