Dear Nick,
The conversion of values from GROMACS to AMBER is correct, however the definition of the section is not...
The Rm value is calculated from the arithmetic mean:
Rm = Rm[1]/2 + Rm[2]/2
while the epsilon is calculated from the geometric mean:
e = sqrt(e[1]*e[2])
Then any of the following definition is correct
# Rm[1]/2 e[1] Rm[2]/2 e[2]
LJEDIT
f H1 1.73585 0.039557 1.73585 0.039557
# Using: (Rm[1]+Rm[2])/2
LJEDIT
f H1 3,47170 0.039557 0.00000 0.039557
# Using: (e[1]*e[2])
LJEDIT
f H1 3,47170 0.001565 0.00000 1.000000
After generating the topology, I strongly advise you to check the parameters using ParmEd.
Best,
Matías
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Nick Palmer" <tuf90798.temple.edu>
Para: amber.ambermd.org
Enviados: Miércoles, 30 de Septiembre 2020 15:46:28
Asunto: [AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT
Hello everyone,
I am looking to convert a Gromacs .itp file to an Amber frcmod file
manually. I have converted the bonded parameters already and I believe that
I have converted the nonbonded parameters as well following this post
http://archive.ambermd.org/201807/0252.html as well as a tutorial I found
about modifying amber14ff. I just wanted to check and make sure I followed
the correct procedure to convert these parameters.
The [atomtypes] parameter I am trying to convert is as follows:
[atomtypes]
F 9 19.00 -0.19 A 3.151e-01 4.170e-01
And my corresponding entry in NONBON is:
f 1.76844 0.099665
And an example of [nonbond_params] is:
F H 1 0.232144 0.165505
F H1 1 0.309293 0.165505
with my corresponding entry in LJEDIT:
f H 1.30287 0.039557 0.00 1.00
f H1 1.73585 0.039557 0.00 1.00
Did I convert these parameters correctly? Thank you in advance.
--
Nicholas J. Palmer
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Received on Thu Oct 01 2020 - 06:00:02 PDT
