Re: [AMBER] Generating the parameters for non-standard amino-acid residue

Date: Mon, 9 Sep 2019 14:01:53 +0000


I am trying to replace an amino-acid residue with a non-standard amino-acid in a short peptide fragment. After optimizing the structure of this non-standard amino-acid, I did run parmchk2 to get the parameters and also did load the frcmod file in tleap. I saved the pdb of the peptide fragment with the replaced amino-acid residue, however, the atom name in the pdb file doesn't match with the ones in the frcmod file, due to which, I guess, the prmtop files are not getting generated. Kindly help.

Rituparna Roy,

Junior Research Fellow,

Department of Chemistry,

Indian Institute of Technology Guwahati.

From: David A Case <>
Sent: 09 September 2019 18:20
To: AMBER Mailing List <>
Subject: Re: [AMBER] Generating the parameters for non-standard amino-acid residue

On Sat, Sep 07, 2019, RITUPARNA ROY wrote:
>I am trying to generate the parameters for a peptide, consisting of a
>non-standard amino-acid. However. I'm getting the following error:
>/home/ritu/softwares/Amber/amber18/bin/teLeap: Error! ** No torsion terms
>for CX-C-N2-CA

Unfortunately, you don't provide nearly enough information for anyone to
be able to help: how did you create the UNIT for the non-standard amino
acid? Did you run parmchk2 to get parameters? If so, does the frcmod
file you created have torsion terms like the one above (and the other
missing terms)? Did you remember to load this frcmod file in your tleap



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Received on Mon Sep 09 2019 - 07:30:02 PDT
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