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

Sat Apr 23 02:40:49 CEST 2016

Applying the same simple conversion to the vdw parameters for atoms Mg+2
(id 46), Ca+2 (id 47), and Zn+2 (id 48) found in amber99.prm of the TINKER
package, which is the base of Sorin parameters, there is agreement between
Mg+2 and Zn+2.

It looks like a bug in the L-J parameters of TINKER package for amber99*
force fields. If it becomes confirmed, should I fill an issue at Redmine or
request a code review?

However I may be wrong...

http://dasher.wustl.edu/tinker/distribution/params/amber99.prm

2016-04-22 20:11 GMT-03:00 Pedro Lacerda <pslacerda+gmx at gmail.com>:

> For me they must be the same in both force fields amber99sb-ildn, amber99,
> at the paper, etc. If it is different then should be another force field,
> isn't it?
>
> About the conversion, I did it wrong on my spreadsheet. Sorry...
>
> It works! Many thanks!
>
> Except for the epsilon of Ca+2. I verified the parameters of atom
> amber99_15  (Ca +2) in ffamber_v4.0/ffamber99sb/ffamber99sbsbnb.itp and, of
> course, is the same of GROMACS files, but it is different than the
> previously referred paper.
>
> I also checked the parameters in amber10.ffparms.tar.bz2/parm/parm99.dat,
> and it agreed with paper, disagreeing with GROMACS.
>
> Just a small question, PARM is the file format for force fields in AMBER,
> right?
>
> http://ffamber.cnsm.csulb.edu/ffamber.php
> http://ambermd.org/dbase.html
>
>
>
> 2016-04-22 19:29 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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