This error always means the same thing - you haven't correctly done your bookkeeping. If you pass your topology to the -p flag of both gmx solvate and gmx genion, it does all the work for you. You can always double check the number of each species by using grep -c on the coordinate file to count how many of each molecule you have and check against what is listed in the topology.

Upto solvation step the #co-ordinates are same.

It starts differing just after genion step.

step 1) I am adding K ions to neutarlise my system

step 2) adding Mg (say 50) and Cl ( 100 ) to study effect of MG on my system.

The difference starts from step 2.

Note : I am using CHARMM36 ff.

Without your commands, there's nothing I can tell you. If you use -p with solvate and genion, there should be no mismatch.

My system is rna ( Mg & K are present in crystal structure)

 The Steps are

gmx pdb2gmx -f system.pdb -o system.gro -water spce

gmx editconf -f system.gro -o system_newbox.gro -c -box 20 20 20

gmx solvate -cp system_newbox.gro -cs spc216.gro -o system_solvated.gro -p topol.top

gmx grompp -f ions.mdp -c system_solvated.gro -p topol.top -o system_ions.tpr

gmx genion -s system_ions.tpr -o system_solvated_ions.gro -p topol.top -pname K -np #ion ( to neutralise nucleic acid )

gmx genion -s system_ions.tpr -o system_solvated_ions.gro -p topol.top -pname MG -np #ion 

gmx genion -s system_ions.tpr -o system_solvated_ions.gro -p topol.top -nname CL -nn #ion 

// I have tried to add both Mg & Cl in single step but it resulted in same error

gmx grompp -f minim.mdp -c ribo_solvated_ions.gro -p topol.top -o ribo_em.tpr

grommp shows the above mentioned error

@ J Lemkul

Found my mistake..

Hi Sunil! Can you please share what was your mistake? I have the same problem, after gmx solvate the topology coordinates do not much with the system.gro coordinates. By the number of atoms that mismatch it would seem that there are 603 water molecules more in topol.top than in system.gro, but this is not the case. Whatever changes I try it is always 1809 more coordinates in topol.top (divided by 3 gives 603 water molecules) The number of SOL molecules inside system.gro and topol.top are the same. However, even if I subtract 603 water molecules from the SOL type in [molecules] in topol.top, I manage to overcome the mismatch in coordinates but the system explodes (which is expectable since teh problem is somewhere else...)

Hi Sunil Kumar,

It would be grateful if you share the mistake you figured out. I am dealing with the same problem right now.

With best regards,

Sofia Kiriakidi

Hi Sifia Kiriakidi

I just found where I was going wrong and I hope this works for you as well.

Follow the commands in order from the genion step:

gmx grompp -f ions.mdp -c solvate.gro -p topol.top -o ions.tpr

gmx pdb2gmx -f solvate.gro -o solvate1.gro -p topol.top -i ions.itp

gmx genion -s ions.tpr -o solvate_ions.gro -p topol.top -pname [cation] -nname [anion] -neutral

gmx grompp -f minim.mdp -c solvate1_ions.gro -p topol.top -o em.tpr