[gmx-users] Adding FE2+ or FE3+ into the system

[Justin Lemkul]

On 1/10/17 12:08 PM, liming_52 wrote:
> Thanks  for your apply. Since the protein I simulated could bind FE ions.
> I want to compare the affinity difference of FE3+ and FE2+ to the protein. How can I solve this problem?

The central challenge here is that, simply put, there is no good way to 
represent these with existing empirical force fields.  Your best bet is probably 
QM/MM of some sort, because representing a transition metal (which is strongly 
polarizable, induces charge transfer, and has a particular coordination 
geometry) is not really reasonable to expect using an additive force field model.

There are some parameter sets (e.g. one developed for CHARMM: 
dx.doi.org/10.1021/jp309150r) based solely on hydration properties, but that's 
not enough necessarily to study interactions with proteins with any real level 
of confidence.

-Justin

> Could you send me the link of the paper you mentioned?
>
>
>
>
>
> --
>
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China
>
>
>
> At 2017-01-11 00:37:49, "Hannes Loeffler" <Hannes.Loeffler at stfc.ac.uk> wrote:
>> 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
>>
>> --
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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

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