[gmx-users] Add CS ions to system

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat May 18 16:02:47 CEST 2013

Hi all,

I want to add CS ions to my system by genion but it seems impossible when go through the EM.

The molecule section in my top file is:
Protein_chain_A     1
Protein_chain_B     1
POPC        238
SOL         20406
NA               681
CL               702
CS               19

The commands to neutralize and adding CsCl are as follow:

Adding ions:
#grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
#genion -s ions.tpr -o system_solv_ions.gro -p topol.top -conc 1 -neutral

Adding 19 pairs of CsCl:

#grompp -f ions.mdp -c system_solv_ions.gro -p topol.top -o ions_CsCl.tpr
#genion -s ions_CsCl.tpr -o system_solv_ions_CsCl.gro -p topol.top -pname CS -np 19 -nname CL -nn 19


And fatal error as I get is:
#grompp -f minim.mdp -c system_solv_ions_CsCl.gro -p topol.top -o minim.tpr
Fatal error:
No such moleculetype CS

But I see the CS ion in residuetypes.dat which exist in my directory :

CS    Ion

So what's the reason? If it is related to the version of applied GROMACS? I am working with 4.5.5 GROMACS and CHARMM 36 FF.

Thanks. Would you give me any suggestions?


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