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

[Pedro Lacerda]

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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> 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
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>