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