[gmx-users] total charge of the system

[Mark Abraham]

On 01/25/11, ahmet yıldırım  <ahmedo047 at gmail.com> wrote:
> Hi,
> 
> In my simulation, total charge of the system is a noninteger number (System has non-zero total charge: 8.000004e+00). I neutralized it with 8 chlorine atoms. 
> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> 
> 
> Fatal error:
> 
> moleculetype CU1 is redefined
> is it some thing wrong?
> 

ions.itp defines molecule types for ions. Molecule types cannot be redefined. When you #included ions.itp GROMACS thought you were doing illegal redefinitions. Look back in the .top to find the original definitions, and then take suitable action.

Mark


> 
> 
> Below is the first and final version of the .top file:
> 
> 
> First topol.top File
> ....
> [ molecules ]
> ; Compound        #mols
> Protein_chain_P     1
> Protein_chain_L      1
> Protein_chain_H     1
> SOL                     10
> SOL                    127
> 
> SOL                    157
> SOL                 41779
> 
> 
> Final topol.top File
> #include "ions.itp"
> 
> [ molecules ]
> ; Compound        #mols
> Protein_chain_P     1
> Protein_chain_L      1
> 
> Protein_chain_H     1
> SOL                     10
> SOL                    127
> SOL                    157
> SOL                 41771
> CL-                         8
> 
> 
> 
> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 
> 
> 
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