[gmx-users] error in producing top file for a structure

Elie M elie.moujaes at hotmail.co.uk
Sat Sep 8 22:29:19 CEST 2012

Dear all,
I am new to GROMACS. I am trying to minimize a structure but first I have to form the pdb file with the correct force field parameters. I am using version 4.0.5 and an OPLSAA force field. The error I am getting is:.......Opening library file /cygdrive/c/Packages/Gromacs/share/gromacs/top/ffOPLSAA-c.tdbProcessing chain 1 (46 atoms, 1 residues)There are 4 donors and 2 acceptorsThere are 0 hydrogen bonds
-------------------------------------------------------Program pdb2gmx, VERSION 4.0.5Source code file: pdb2gmx.c, line: 429
Fatal error:Atom C in residue LI 1 not found in rtp entry with 1 atoms             while sorting atoms-------------------------------------------------------
I read about the error but i could not figure out the "mismatch" that was stated in the input file which you will find attached. Please can anyone help me
ThankssN.B: The pdb format of the inout file is produced using OPENBABEL.
Elie MUniversity of NottsNG7 2RDUK


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