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

CROUZY Serge 119222 serge.crouzy at cea.fr
Tue Jan 10 17:24:51 CET 2017

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
sig = (A/C)^1/6
eps=C^2 / (4 A)
For Zn sig=0.168112  eps=4.631677 kJ/mol

But no Fe2+


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

-----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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