Hi,
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.
Best
On Friday, October 26, 2018, 8:24:35 PM GMT+2, Matias Machado <mmachado.pasteur.edu.uy> 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: [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 Nov 02 2018 - 10:00:01 PDT
