[gmx-users] peptide ligand

‪farial tavakoli‬ ‪ farial.tavakoli at ymail.com
Tue Oct 3 10:26:38 CEST 2017

Dear GROMACS users
I need to run a MD on my Protein-peptide ligand complex in GROMACS. I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes] was Protein_chain_B) and converted it to .itp file to string it in Protein.top file, then, added Protein_chain_B in [ molecules ] directive to create one topology file for my complex. Created newbox and solvate. 
But when I gave this command:gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr

I faced to this error:

Group Protein_chain_B referenced in the .mdb file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option
of grompp.

In spite of , my ligand [ moleculetypes ] in the ligand.itp file is Protein_chain_B , but GROMACS gives error. 
Would you please advice me how can I solve this problem?


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