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
database.
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 !
XAvier
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