[gmx-users] Adding FE2+ parameters

Tue Jan 10 18:27:10 CET 2017

Hi,

They've been there in the GROMOS forcefield implementations in GROMACS ever
since Peter Tieleman's commit in 1999. If GROMOS themselves have never
documented them, then that is worrying to the point of "do something else."
A publication using any transition-metal parameterization without detailed
commentary about why it might be a valid model would get at least a "please
explain" from me as a reviewer...

Mark

On Tue, Jan 10, 2017 at 6:19 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/10/17 12:09 PM, CROUZY Serge 119222 wrote:
> > Hello Hannes
> >
> > I'm perfectly aware how you need to be careful in using metal parameters
> - checking for which solvent and which coordination they have been created
> for.
> > In my case structural metal coordinated to protein amino acids...
> > I did try to see in Li/Merz parameters which line could resemble the
> parameters in Gromacs for Zn2+ but with no success - This brings me back to
> the original question, where do Zn parameters in Gromacs 54a7 come from ?
> Knowing this I could try deduce parameters for Fe2+
> >
>
> This came up recently, and the best answer that I found was: these
> parameters
> have simply always existed in GROMOS.  The only reference I could find was
> the
> GROMOS manual itself, which requires payment of a license fee to even
> read.  If
> that's not correct, someone please speak up!
>
> -Justin
>
> > Thanx
> >
> > Serge Crouzy PhD HDR
> > Groupe de Modélisation et Chimie Théorique
> > Laboratoire de Chimie et Biologie des Métaux
> > Institut de Biosciences et Biotechnologies de Grenoble
> > CEA Grenoble  UMR  CEA/CNRS/UJF 5249
> > 17, rue des martyrs
> > 38054 Grenoble Cedex 9
> > Bat. K  pièce 110
> > Tel (33)0438782963
> > Fax (33)0438785487
> > http://big.cea.fr/drf/big/CBM/GMCT
> >
> >
> >
> >
> > -----Message d'origine-----
> > De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] De la part de Hannes
> Loeffler
> > Envoyé : mardi 10 janvier 2017 17:38
> > À : gromacs.org_gmx-users at maillist.sys.kth.se
> > Cc : gmx-users at gromacs.org
> > Objet : Re: [gmx-users] Adding FE2+ or FE3+ into the system
> >
> > What are you planning to do with those parameters?
> >
> > You could have a look into the Li/Merz parameters (and papers!)
> available with the AmberTools (may not have been converted yet to Gromacs
> formats and the 12-6-4 sets would need support in the code).
> > Generally, you should be wary when using simple ion force fields and
> check carefully how they have been parameterised and what for.
> > Distinguishing different valencies of the same transition metal atom
> with only vdW/Coulomb parameters will most likely not capture their complex
> chemistry.
> >
> >
> > On Tue, 10 Jan 2017 16:24:47 +0000
> > CROUZY Serge 119222 <serge.crouzy at cea.fr> wrote:
> >
> >> I'm interested as well in knowing how to get decent parameters for
> >> Fe2+
> >>
> >> From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp
> >> We have Zn2+  (What is a reference for these parameters ?)
> >>
> >> name   bondtype   mass   charge   ptype     C                A
> >> ;name  at.num   mass      charge  ptype       c6           c12
> >> ZN2+   30      0.000      0.000     A  0.0004182025  9.4400656e-09
> >>
> >> From which I deduced
> >> if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6 to be compared to
> >> the standard V=4*eps*[(sig/r)^12 - (sig/r)^6] A =4*eps*sig^12
> >> C=4*eps*sig^6
> >> sig = (A/C)^1/6
> >> eps=C^2 / (4 A)
> >> For Zn sig=0.168112  eps=4.631677 kJ/mol
> >>
> >> But no Fe2+
> >>
> >> Regards
> >>
> >> Serge Crouzy PhD HDR
> >> Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et
> >> Biologie des Métaux Institut de Biosciences et Biotechnologies de
> >> Grenoble CEA Grenoble  UMR  CEA/CNRS/UJF 5249 17, rue des martyrs
> >> 38054 Grenoble Cedex 9
> >> Bat. K  pièce 110
> >> Tel (33)0438782963
> >> Fax (33)0438785487
> >> http://big.cea.fr/drf/big/CBM/GMCT
> >>
> >>
> >>
> >> -----Message d'origine-----
> >> De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> >> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] De la part
> >> de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À :
> >> gmx-users at gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into
> >> the system
> >>
> >> Dear gromacs users,
> >>
> >> I want to compare the protein in the buffers with FE2+ and FE3+,
> >> respectively.
> >>
> >> How can I add FE2+ or FE3+ into the system? What is the command?
> >>
> >> Thanks in advance.
> >>
> >>
> >>
> >>
> >>
> >> --
> >>
> >> With my best wishes,
> >> Ming Li, PhD
> >> Chinese Academy of Agricultural Sciences, Beijing, China
> >
>
> --
> ==================================================
>
> 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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