Great thank you, that was exactly what I was looking for!
How should I use parmed to check the parameters?
I imagined that I would use parmed to convert the parameters that I
manually created to a gromacs top file and then compare them with the
original itp file. I did that and thankfully everything seems to be
matching with what was converted. However, it didn't seem like the LJEDIT
parameters were converted back to [nonbond_params]. Is the LJEDIT
conversion not implemented because it is a much less used feature, or did I
miss an option when I was converting it? Thank you again!
On Thu, Oct 1, 2020 at 8:59 AM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> 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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>
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>
--
Nicholas J. Palmer
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Received on Thu Oct 01 2020 - 16:30:02 PDT
