Dear Hosein,
I guess it may be possible, but I've never tried... certainly Jason Swails or others can give better insight than me on that... just in case, check you are modifying the specific atom bonded parameters and not the atom type related parameters... you can use commands "printBonds", "printAngles" and "printDihedrals" for that...
Best,
Matías
----- Mensaje original -----
De: "hosein geraili" <geraili_hosein.yahoo.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 7 de Noviembre 2018 5:31:31
Asunto: Re: [AMBER] non-bonded params
Is it possible to use setangle of parmED in this case? Because I need to change so many angles that is not possible to define new atom type for each of them. If yes, do you know any tutorial or good document that I could use as a guide?Best
On Friday, November 2, 2018, 8:12:20 PM GMT+1, Matias Machado <mmachado.pasteur.edu.uy> wrote:
Dear Hosein,
In GROMACS you can set specific bonded parameters in the rtp file which overwrite the atom types definitions. However in AMBER you can not do that. So you will need to add new atom types to set particular bonded parameters although from a non-bonded point of view they may be the same...
Best,
Matias
----- Mensaje original -----
De: "hosein geraili" <geraili_hosein.yahoo.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Viernes, 2 de Noviembre 2018 13:50:47
Asunto: Re: [AMBER] non-bonded params
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 09 2018 - 08:00:03 PST
