[gmx-users] total charge of the system
Mark Abraham
mark.abraham at anu.edu.au
Tue Jan 25 12:13:57 CET 2011
On 01/25/11, ahmet yıldırım <ahmedo047 at gmail.com> wrote:
> Dear Mark and Emanuel,
>
> I am sending the ions.tip and the topol.top files. Everything seems ok. Any problem about these files?
>
No. So one of the other #include files is erroneously defining ion molecule types. See www.gromacs.org/Documentation/Include_File_Mechanism. Go and read them and fix it.
As the link I sent last time hinted, you need to name *molecules* in the [molecules] directive. Look carefully at the *molecule* name of chloride where it is defined.
Mark
>
>
>
> By the way, I am using the Gromacs 4.5.3.
> Force Field 43a1
>
> 25 Ocak 2011 12:03 tarihinde Emanuel Peter <Emanuel.Peter at chemie.uni-regensburg.de> yazdı:
>
>
> > Hello,
> >
> > You have to look into your ions.itp which is included in your top-file by #include ions.itp.
> >
> > There all the types of ions have to be defined.
> > The atom-types which you can see in the ions.itp, you will
> > find in the ff"your-forcefield".itp where your atomtypes are defined.
> > On top of your .top file the Atomtype-itp-file is included.
> >
> > All these files are normally placed in /usr/share/gromacs/top/.
> > But you also can place them into your current directory.
> >
> > Bests,
> >
> > Emanuel
> >
> > >>> Mark Abraham 25.01.11 10.48 Uhr >>>
> >
> >
> >
> >
> >
> > 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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> > > >
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> > > >
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> > >
> > >
> > >
> > > --
> > > Ahmet YILDIRIM
> > >
> > >
> > >
> >
> >
> >
> >
> >
> >
> > --
> >
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> >
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>
> --
> Ahmet YILDIRIM
>
>
>
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