Antw: Re: [gmx-users] total charge of the system

[Emanuel Peter]

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   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

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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