[gmx-users] peptide ligand

Justin Lemkul jalemkul at vt.edu
Tue Oct 3 15:05:52 CEST 2017

On 10/3/17 4:26 AM, ‪farial tavakoli‬ ‪ wrote:
> 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.

You shouldn't have to do any topology manipulation. pdb2gmx handles multiple 
chains natively without any additional effort on your part.


> 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?
> Best
> Farial


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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