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

[liming_52]

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?
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
>
>-- 
>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.