[gmx-users] Regarding simulation of ions-water system

[Dilip H N]

Hello,
I want to simulate Ca2+, CO32- ions in the water system. So these were the
following commands i followed:
gmx editconf -f abc.gro -box xxx -o def.gro
gmx insert-molecules -f def.gro -ci ghi.gro -nmol x -o jkl.gro
gmx solvate -cp jkl.gro -cs scp216.gro -o mno.gro
gmx pdb2gmx -f mno.gro -o mno.pdb (to generate topology)
gmx grompp -f ions.tpr -c mno.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o pqr.gro -p topol.top -pname CAL -np xx
I hope these are the proper ways to generate topology and add ions and to
set up the system...(Any modifications are appreciated.)

And when i gave the energy minimization command (gmx grompp -f em.mdp -c
pqr.gro -p topol.top -o em.tpr), i am getting the following error:

Excluding 3 bonded neighbours molecule type 'Other'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Ion2'
turning H bonds into constraints...
Removing all charge groups because cutoff-scheme=Verlet

Atom 1 'CAL' in moleculetype 'Ion2' is not bound by a potential or
constraint to any other atom in the same moleculetype.

Atom 2 'CAL' in moleculetype 'Ion2' is not bound by a potential or
constraint to any other atom in the same moleculetype.....

how to resolve this error..?? (Is this because of the cutoff scheme..?? )

Any suggestions are highly appreciated.

-- 
With Best Regards,

DILIP.H.N
Ph.D. Student



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