[gmx-users] Heme group in the forcefield gromos53a6

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 18 21:04:23 CET 2011

Tanos Celmar Costa Franca wrote:
> Dear users,
> We are trying to perform a MD simulation of a protein with a heme group 
> using the gromos53a6 force field but when trying to run grompp we 
> receive the error mesage:
> Program grompp, VERSION 4.0.3
> Source code file: ../../../../src/kernel/toppush.c, line: 947
> Fatal error:
> Atomtype FE2+ not found
> How can it happen if the gromos53a6 force field have parameters to the 
> heme group ?
> Does someone knows how to fix it ?

Heme parameters are included in 53A6, but they don't make reference to any such 
"FE2+" atomtype.  The .rtp and .atp files specify an "FE" atomtype, though. 
You're still probably going to run into missing bonded parameters for the 
connection between your protein and heme.  I don't know what the solution for 
that is, though.

Also, unless you have a specific reason for using a Gromacs version that is two 
years old (as of today, exactly!) then you should upgrade to a more recent 
(preferably the most recent) version, to take advantage of numerous bug fixes 
and feature additions.



> Tanos Celmar Costa Franca - D.Sc
> Coordenador do Programa de Pos-graduacão em Química
> Secão de Engenharia Química - SE/5
> Instituto Militar de Engenharia - IME
> Rio de Janeiro - RJ
> Brasil
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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