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. Diane
________________________________ De: [EMAIL PROTECTED] de la part de Absalom Zamorano Date: mar. 2006-05-09 09:01 À: gmx-users@gromacs.org 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 combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations 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 ___________________________________________________________ Do You Yahoo!? La mejor conexión a Internet y <b >2GB</b> extra a tu correo por $100 al mes. http://net.yahoo.com.mx _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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