[gmx-users] Adapting metallic ions from AMBER to GROMACS

[Pedro Lacerda]

Hi Mark,

I starting converting from AMBER (according to the paper) to GROMACS and
comparing the results.

Please explain in more words what this constant of two mean or how can I
handle it. Ignoring it and just converting the units, I got these results

AMBER (table 2a)
Rmin/2 (Å) epsilon (kcal/mol)
Zn2+ 1.10E+00 1.25E-02
Mg2+ 7.93E-01 8.95E-01
Ca2+ 1.71E+00 4.60E-01
AMBER converted
R (nm) epsilon (kJ/mol)
Zn2+ 2.20E+01 5.23E-02
Mg2+ 1.59E+01 3.74E+00
Ca2+ 3.43E+01 1.92E+00

amber99sb-ildn.ff/ffnonbonded.itp
sigma (nm) epsilon (kJ/mol)
Zn2+ 1.96E-01 5.23E-02
Mg2+ 1.41E-01 3.74E+00
Ca2+ 3.40E-01 3.60E-01

I got exact matches for epsilon in Zn and Mg, but not for Ca.  Also the
difference on sigma was in the order Å/10, except for Zn which was
relatively significant.

(I'm expecting that Mailman render the table into plain text relatively
well, so if this post go with bad formatting I'll post again)

Very thanks
Pedro


2016-04-18 21:29 GMT-03:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Convert the units and absorb the factor of two to the minus six. Compare
> with other ions present in both representations of such force fields.
>
> Mark
>
> On Tue, 19 Apr 2016 02:21 Pedro Lacerda <pslacerda+gmx at gmail.com> wrote:
>
> > Hi Gromacs users,
> >
> > We are planning a simulation with a metallic (fe+2) attached on the
> > protein. The parameters found in [1] cannot be directly inserted on
> > ffnonbonded.itp because equation 1 of [1] and equation 4.5 of [2] are
> > slightly different.
> >
> > Theoreticaly these Lennard-Jones parameters could be used in any PME
> based
> > force field, but it was derived and tested using the AMBER software and
> > potential, so it is our current force field of choice. In
> > amber99sb-ildn/ffnonbonded.itp the long range interactions are described
> in
> > terms of epsilon (kJ/mol) and sigma (Rmin; nm).
> >
> > Eq 1:
> >
> >     Lj = 4e ((R/r)^12 - (R/r)^6)
> >
> > Eq 4.5:
> >
> >     Lj = e ((R/r)^12 - 2(R/r)^6)
> >
> > Seems that Rmin values are written as Rmin/2 in AMBER files avoiding some
> > calculations to optimize the software. But this occurs at implementation
> > level and probably does not have correspondence with the paper.
> >
> > My question is how can I adapt these parameters so they can be used in
> > Gromacs?
> >
> > (Sorry about the previous email, now the title is correct)
> >
> > [1]
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728907/pdf/nihms481931.pdf
> >
> > [2] ftp://ftp.gromacs.org/pub/manual/manual-5.1.2.pdf
> >
> > [3] http://comments.gmane.org/gmane.science.biology.gromacs.user/82242
> >
> >
> > Cheers,
> >
> > Pedro Lacerda
> > --
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