[gmx-users] pdb2gmx residue error

X.Periole X.Periole at rug.nl
Sat Jul 29 10:45:03 CEST 2006

> I am trying to do a simple NaCl solvation and MD run 
>using GROMACS. I have 4 atoms in my (.xyz) file for the 2 
>Na's and 2 Cl's. I convert the (.xyz) to (.pdb) using 
>babel. Afterwards, I try to generate the topology file 
>using pdb2gmx program and it generates an error.  I am 
>using the 43a1 force field.
>FATAL ERROR: Residue "LIG" not found in residue topology 

What does LIG represent in your pdb file ??

The best way would probably be to first construct a
box of water (editconf, genbox) and then put ions inside,
manually by removing water molecules or using genion !


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