Hi,
Maybe you can try parmed for your case.
Xparmed is also available to modify the prmtop file. For detail
informations. Please read the mannual.
Best regards
-------- åå§é®ä»¶ --------
主é¢：Re: [AMBER] non-bonded params
å件人：hosein geraili
æ¶ä»¶äºº：AMBER Mailing List
æé：
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 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,
MatÃas
------------------------------------
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"
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     Â
 sigma    epsilon O21    K      1   Â
   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 - 16:30:02 PDT
