Re: [AMBER] FATAL Error Issue

From: Amara Jabeen via AMBER <>
Date: Mon, 26 Sep 2022 08:06:00 +0000

Hi Tamsila
Are you using forcefield for small molecules? e.g. if you are using tleap for generating ligand topology have you used source leaprc.gaff?
From: Tamsila Parveen via AMBER <>
Sent: Monday, September 26, 2022 5:56 PM
To: David A Case <>
Cc: AMBER Mailing List <>
Subject: Re: [AMBER] FATAL Error Issue

Dear Sir,
I have loaded the same libraries, the residues are same in the ligand
libraries as mentioned in complex file. Kindly resolve the issue


On Wed, Sep 21, 2022 at 5:19 PM David A Case <> wrote:

> On Wed, Sep 21, 2022, Tamsila Parveen via AMBER wrote:
> >There is an issue when I am saving amberparams for prmtop and inpcrd
> files,
> >amber does not read ligand molecules' few atoms in complex file and
> >generate following errors
> >
> >FATAL: Atom .R<UNL 740>.A<N 1> does not have a type.
> >FATAL: Atom .R<UNL 740>.A<C 2> does not have a type.
> >FATAL: Atom .R<UNL 740>.A<O 3> does not have a type.
> >FATAL: Atom .R<UNL 740>.A<F 4> does not have a type.
> >FATAL: Atom .R<UNL 740>.A<S 5> does not have a type.
> We would need more details to be of any help. The messages above generally
> arise when you have atoms in your input pdb file (such as residue UNL, atom
> N, etc) that are not present in the ligand libraries that you created.
> Make
> sure the residue and atom names in the pdb file exactly match those in
> whatever libraries you loaded.
> ....hope this helps....dac

*Tamsila Parveen*
Department of Biosciences
COMSATS University, Sahiwal Campus
COMSATS Road, Off GT Road, Sahiwal
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Received on Mon Sep 26 2022 - 01:30:04 PDT
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