Dear Nick,
There is no need for back converting AMBER to GROMACS, you can simple use the command "printLJMatrix" to retrieve the pair list interactions directly from the prmtop.
Be aware that there are some limitations regarding format conversions by ParmEd. Jason Swails (the principal developer) is the right person to answer that... In any case, I suggest you to carefully read the manual.
Best,
Matías
----- Mensaje original -----
De: "Nick Palmer" <tuf90798.temple.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 1 de Octubre 2020 20:16:21
Asunto: Re: [AMBER] [External] Re: Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT
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 Sat Oct 03 2020 - 09:30:03 PDT
