Re: [AMBER] parameterization using antechember

From: Hannes Loeffler <>
Date: Fri, 30 Jan 2015 12:16:12 +0000

Your list of atoms is certainly covered by the AM1 method used in sqm
to compute AM1/BCC charges. If they weren't you could still get
charges at a high level of theory, e.g. RESP. But this is no really
sufficient information. What you need to check is if your molecules is
covered by the chemical space covered by the GAFF force field described
in the respective publication.

You don't say what commands you have used in leap. Loading the frcmod
file alone is not sufficient. You also need to load the second file
you have created with antechamber: probably a mol2 file or maybe prep.

On Fri, 30 Jan 2015 14:07:39 +0200
Debasish Mandal <> wrote:

> Hi,
> I want to prepare a parameter file for a organic molecule
> using antechamber. The molecule possesses C H O N P and Cl atom. Is
> it possible to make it using antechamber?
> I have tried to do it and a frcmod file has been prepared. But when I
> have tried to run leap it shows the following error with unsuccessful
> parameterization of the protein.
> FATAL: Atom .R<RFO 474>.A<P 30> does not have a type.
> FATAL: Atom .R<RFO 474>.A<O 31> does not have a type.
> FATAL: Atom .R<RFO 474>.A<N 32> does not have a type.
> FATAL: Atom .R<RFO 474>.A<C 33> does not have a type.
> FATAL: Atom .R<RFO 474>.A<H 34> does not have a type.
> FATAL: Atom .R<RFO 474>.A<Cl 35> does not have a type.
> Could you please help me to solve this problem?
> Thanks & Regards
> Debasish
> The Hebrew University, Jerusalem
> Israel
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Fri Jan 30 2015 - 04:30:04 PST
Custom Search