Re: [AMBER] non-bonded params

From: hosein geraili <>
Date: Fri, 2 Nov 2018 16:50:47 +0000 (UTC)

Thank you for your help. I have another question that I would be grateful if somebody help.
I need to change the angle values for all the angles in a ligand inside a protein. In the .frcmod file I only can change the values of atom types for example FE-S-FE, but If I need to have a different value for FE1-S1-FE2 and FE1-S2-FE2, it is not possible to implement it through frcmod.  How can I do that? I tried to do it through .prmtop, but it is impossible, too.
    On Friday, October 26, 2018, 8:24:35 PM GMT+2, Matias Machado <> wrote:
 Dear Hosein,

You can add those interactions at the LJEDIT section, which can be defined at the bottom of a parameter file (i.e. frcmod), see the following threat from the AMBER mailing list: []

# Sections' order in parameter file







Or you can patch the topology using Parmed (See Manual: in particular commands "addLJtype" and "changeLJPair"), but be aware of the difference in atom-type and vdW-type definition.



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "hosein geraili" <>
Enviados: Viernes, 26 de Octubre 2018 13:30:36
Asunto: [AMBER] non-bonded params

Hi all,I need to use a scaling factor on the result of the Loerntz-Berthelot combination rule on two different atoms inside a protein. I found the force field files in the $AMBERHOME directory, but I don't know how to do this particular action. In Gromacs, I would add:

[ nonbond_params ];i         j           func             sigma       epsilon O21        K           1             number  number
in the ffnonbonded.itp, but I don't know how to do it in Amber.
Any idea on how to do this?
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Received on Fri Nov 02 2018 - 10:00:01 PDT
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