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

[Pedro Lacerda]

Thank you!

According to [1, Table 2a], these are the L-J (6-12) parameters for Ca2+
used at AMBER package. Or the paper or GROMACS copied wrongly from the
AMBER package source because simple unit conversion gives different results.

I don't own a copy of AMBER package, please could you verify the Ca L-J
parameters for me?

And I can't see how your conversion formula from Rmin/2 to sigma could
produce the right result.

[1] J Chem Theory Comput. 2013 June 11; 9(6): 2733–2748.
doi:10.1021/ct400146w.

2016-04-21 23:35 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 4/21/16 4:30 PM, Pedro Lacerda wrote:
>
>> 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
>>
>>
> It's force field convention, just different notation.  Sometimes different
> force fields or programs use Rmin/2, Rmin, or sigma.  They're easily
> converted, e.g.:
>
> sigma = (Rmin/2)*2*2^(-1/6)
>
> and in GROMACS the units are nm so you need an additional multiplication
> by 0.1 to convert A -> nm.
>
> 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.
>>
>>
> See above for the proper way to convert Rmin/2 to sigma.
>
> As for Ca, probably the parameters are coming from a different source.  I
> don't know what "Table 2a" means or what paper it's from, but you need to
> verify that the source of parameters is compatible or that you understand
> where differences are coming from.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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>
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