Re: [AMBER] Parameters for non-standard residues

From: Nagar, Hemant <>
Date: Tue, 19 Oct 2021 20:44:59 +0000

I went through the tutorial of antechamber to generate force field parameter for nonstandard residues. I have following questions-
a) how to generate mol2 file for two conformations(alpha and beta)? These two conformation are for the particular molecule that is given in the tutorial or we need to generate these two conformation for every nonstandard fragment?
In my case DAL,ACB are the nonstandard residues?
I found following command on AMBER tutorials to generate mol2 files-
antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
I can save my nonstandard residue in different file and using this command I can generate mol2 file but how I can generate two mol2 files?

b) After following the procedure that is given in the tutorial of antechamber, how I can generate library file for that particular nonstandard residue?

Hemant Ngar

-----Original Message-----
From: David A Case <>
Sent: Monday, October 18, 2021 4:54 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Parameters for non-standard residues

On Mon, Oct 18, 2021, Nagar, Hemant wrote:

>I want to generate force field parameters for nonstandard residues .

Aargh: the Amber tutorial pages on this subject are not as helpful as they should be. While it would be great to make a completely new tutorial, two existing pages are rather hard to find:

1. Tutorial 5.3 is the main "standard" tutorial for making a modified amino acid. But it is listed under "Introductory case studies", and needs a cross-link under "Developing non-standard parameters".

2. Although they are quite old, the original antechamber tutorials are still very helpful:;;sdata=Uwb6lT4cEbetiJGNAISAUPLl9il7u68UF4hDEOmT1XU%3D&amp;reserved=0. Look at example 2, "Generate residue topology files for non-standard amino-acid residues".

I'm hoping Maria can add making some new links to here webpage "to-do" list.

...good luck...dac

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Received on Tue Oct 19 2021 - 14:00:02 PDT
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