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

[Justin Lemkul]

On 4/22/16 6:24 PM, Pedro Lacerda wrote:
> 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.
>

That paper was published 3 years after AMBER99SB-ILDN so expecting those 
parameters to be in that force field implementation is wrong.  There could be a 
mistake but the AMBER ports have been extensively verified.  There are lots of 
AMBER-compatible ion parameters floating around, though.

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

The AMBER force fields should be freely available (I don't use AMBER software).

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

Plug in the values, it works.  It's the same conversion for CHARMM.  For 
instance, Mg2+:

1.1 * 2 * 2^(-1/6) * 0.1 = 0.196

-Justin

> [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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-- 
==================================================

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

==================================================