Re: [AMBER] Adapting angle parameters for new angles

From: Christian Seitz via AMBER <amber.ambermd.org>
Date: Tue, 8 Jul 2025 19:00:10 +0000

Hi Timothy,

Thanks for the suggestions, I made an frcmod file instead of changing the official parameter file and added in all of my custom parameters. I can build the system as expected now~

best,
Christian

Christian Seitz
PhD, Dept. of Computer Science | UChicago
cgseitz.uchicago.edu<mailto:cgseitz.uchicago.edu>
[www.linkedin.com/in/christianseitz21]<http://www.linkedin.com/in/christianseitz21>
________________________________
From: Timothy Giese <giese025.rutgers.edu>
Sent: Monday, July 7, 2025 14:07
To: Christian Seitz <cgseitz.uchicago.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Adapting angle parameters for new angles

You could write a separate frcmod file to extend (or change) the force field parameters rather than modifying the official parameter file. Here is a link describing the frcmod file format:
 https://ambermd.org/FileFormats.php#frcmod<https://urldefense.com/v3/__https://ambermd.org/FileFormats.php*frcmod__;Iw!!BpyFHLRN4TMTrA!5OZDyDzR81fZhXTP6oE44QSRcNB6_xQVlZHpRI_wiemTJlvx73SL1YHHmTdXdDytj04EVkMsstKGBjdGnW70Ckx0$>

Here is an example:
"""
Remark line goes here
MASS

BOND

ANGLE
Os-Cg-Cy 70.00 108.50

DIHE

IMPROPER

NONBON

"""

To incorporate this in the tleap input, you'd load the force field parameters as normal, then add the command "loadamberparams my_custom_params.frcmod" before reading the pdb file.

Although this may not be directly relevant to your situation, one often encounters frcmod files when parametrizing small drug-like molecules using antechamber and parmchk2. The parmchk2 program is used to write a frcmod file that contains guesses for the missing parameters. An example can be found in the tutorial linked below. Note that the default behavior of parmchk2 is to look for parameters missing from the gaff force field; use the --help option for additional info.
https://ambermd.org/tutorials/basic/tutorial4b/index.php<https://urldefense.com/v3/__https://ambermd.org/tutorials/basic/tutorial4b/index.php__;!!BpyFHLRN4TMTrA!5OZDyDzR81fZhXTP6oE44QSRcNB6_xQVlZHpRI_wiemTJlvx73SL1YHHmTdXdDytj04EVkMsstKGBjdGnQCTJFra$>

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Received on Tue Jul 08 2025 - 12:30:02 PDT