[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?





--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



At 2017-01-11 00:24:47, "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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