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.
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.0.x
-Justin
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
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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