[gmx-users] error: group protein not found in index file

Justin Lemkul jalemkul at vt.edu
Sun Oct 14 04:35:17 CEST 2012

On 10/13/12 10:32 PM, Liu, Hanzhong wrote:
> Hi All:
>      I'm trying to set up a small box with only water and ions (no protein) and run MD simulation. The commands I used to set up my system and running MD are as follows:
>      genbox -cs spc216.gro -o water.gro -maxsol 256 -box 2.1 2.1 2.1
>      pdb2gmx -f water.gro -q water.pdb -n index.ndx
>      grompp -f ions.mdp -c water.gro -p topol.top -o ions.tpr
>      genion -s ions.tpr -o water_ions.gro -pname NA -nname CL -nn 23 -np 23 -rmin 0.44 -p topol.top
>      grompp -f mini.mdp -c water_ions.gro -p topol.top -o em.tpr
>      mdrun -v -deffnm em
>      grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
> And then I received the error message
> Fatal error:
> Group Protein not found in 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.
> Then I tried using make_ndx -f water_ions.mdp -o index.ndx to generate index file and tried grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr - index.ndx but still didn't work. In my system, there is no protein, so how can I setup the system correctly and run MD. Thanks!

If there is no protein, don't specify "Protein" anywhere in your .mdp file. 
Likely this is one of your tc-grps.  You should probably be using "System" for 
this setting.


> --------------------------------------------------------------------------------------------
> what's in top file:
> [ system ]
> ; Name
> Generated by genbox
> [ molecules ]
> ; Compound        #mols
> SOL         210
> NA               23
> CL               23


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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