RE : [gmx-users] Fatal error: moleculetype SOL is redefined.

Diane Fournier diane.fournier at
Wed May 10 17:38:24 CEST 2006

I had the same problem once, and it turned out that I had mistakenly put information about my ligand molecule in the "moleculetype" section of my enzyme topology file. That info is also given in the .itp files that are included into your peptide topology file (at the end of the file for ions and solvent), so grompp sees two definitions for the same molecule type. The number and type of solvent molecules must be included in the "molecule" section of the topology (completely at the end of the the .top file).
What is strange, though, is that genbox usually puts that information automatically in the .top file that it generates. My advice is to check your topology file. 


De: gmx-users-bounces at de la part de Absalom Zamorano
Date: mar. 2006-05-09 09:01
À: gmx-users at
Objet : [gmx-users] Fatal error: moleculetype SOL is redefined.

Hi gromaxers, I want to generate a tpr file for a
minimization. I have 3 peptides in water and Im using
OPLS ff, but after I run grompp, system backs me the
next message:
creating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 332520 of the 332520 non-bonded parameter
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter
Excluding 3 bonded neighbours for Protein_X 1
Cleaning up temporary file gromppDDYIem
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 887

Fatal error:
moleculetype SOL is redefined
Some commentary will be very appreciated.
Thank you for advance.

Dr. Absalom Zamorano Carrillo
Profesor Titular A
Programa Institucional de Biomedicina Molecular, ENMyH-IPN
Guillermo Massieu  Helguera  #239 Fracc. "La Escalera"
Ticomán, D.F. México, C.P  07320
Tel. (55) 57296000,  ext 55542

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