[gmx-users] Error in grompp for protein-ligand tutorial

[José Adriano da Silva]

 I am new to Gromacs, then follow the tutorial protein-ligand, decided to
adapt the procedure for my protein (acetylcholinesterase) and my binder. The
procedure is this (protein-ligand complex): 

 

 
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/comp
lex/index.html>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl
ex/index.html 

 

Well, I switched to facilitate the name of my protein and my binder by the
names used in the tutorial. The problem occurs when I do the command: 

 

grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

 

 

The following error occurs: 

 

Fatal error: 

Molecule type 'Protein_chain_A' contains no atoms 

 

 

I do not know how I can fix .... so please help me.