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: [http://archive.ambermd.org/201807/0247.html]
# Sections' order in parameter file
MASS
BOND
ANGL
DIHEDRAL
IMPROP
NONB
LJEDIT
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.
Best,
Matías
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/laboratorios-eng/lsbm]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "hosein geraili" <geraili_hosein.yahoo.com>
Para: amber.ambermd.org
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?
Best
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Received on Fri Oct 26 2018 - 11:30:02 PDT
