[gmx-users] total charge of the system

[Mark Abraham]

On 01/25/11, ahmet yıldırım  <ahmedo047 at gmail.com> wrote:
> Dear Mark,
> 
> I looked at gromacs mail list but I could not find a proper solution .What should I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files
> 
> 
> I have error as the following reconstructed1 .top file:
> 
> Fatal error:
> 
> moleculetype CU1 is redefined
> 
> 
> I have error as the following reconstructed2 .top file:
> 
> Fatal error:
> 
> No such moleculetype CL-
> 
> 

I don't have any knowledge of the context, so can't answer. It looks to me like you are mixing copies of ions.itp from multiple sources. Don't. Use the one for the force field you are targetting. pdb2gmx generated the right invocation - all you should have to do is use that by generating correctly-named ions. See http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion)

Mark


> Original .top file:
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound        #mols
> Protein_chain_P     1
> Protein_chain_L     1
> Protein_chain_H     1
> SOL                10
> SOL               127
> SOL               157
> SOL             41779
> 
> 
> reconstructed1 .top file
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> #include "ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ 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
> reconstructed2 .top file
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ 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
> 
> 
> 25 Ocak 2011 10:49 tarihinde Mark Abraham <mark.abraham at anu.edu.au> yazdı:
> 
> > 
> > 
> > 
> > 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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> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 
> 
> 
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