Re: [AMBER] NEW parameters with AMBER

From: Anna Cebrian Prats <>
Date: Thu, 14 Jul 2016 13:52:43 +0000


Thank you for your answear.

I have calculated with gaussian de charge distribution of a HEM interacting with a HID. With this calculation I have obtained a .gesp file. This file I have used antechamber to obtain the ac file and espgen to obtain the *.esp file. My objective is to create a prep file for the HID residue and a prep file for the HEM structures. Then create a frcmod file to define the corresponding parameters.

antechamber -i *.gesp -fi gesp -o *.ac -fo ac -j 1 -at amber -pf y

I already obtain using residuegen the prep file for the HID residue. However I don't know how to define the prep for only the HEM structure and the corresponding frcmod parameters for the all HEM-HID structure.

What suggestions do you have to perform that?

Thank you


De: David A Case <>
Enviat el: dijous, 14 de juliol de 2016 13:59:06
Per a: AMBER Mailing List
Tema: Re: [AMBER] NEW parameters with AMBER

On Thu, Jul 14, 2016, Anna Cebrian Prats wrote:
> I have performed a HF calculation in order to obtain a gesp file.
> This file I have used antechamber to obtein a 'ac' file.
> With this file I want to obtain a prepi file and his corresponding frcmod

We would need to know what antechamber command you used to obtain the ac
file. But, if you are happy with the charges and atom types in the ac file,
antechamber can do file format conversions, e.g.:

antechamber -fi ac -i <> -fo prepi -o <file.prepi>

The parmchk2 program can then be used to obtain the frcmod file.

However, I'm concerned about what you wrote:

1. 'ac' files are generally only intermediates created by antechamber; most
workflows never deal with these files directly. This is why I am wondering
how you obtained the ac file, and why.

2. The prepi format is only there for backwards compatibility. Consider
using mol2 instead. For example, you can directly visualize mol2 files in
most visualization programs, and it is much easier to understand (and
potentially modify) the information in them.


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