[gmx-users] total charge of the system

[ahmet yıldırım]

Dear Mark,

I looked at gromacs mail list but I could not find a proper solution
.Whatshould
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-
*
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             4177*1*
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             4177*1*
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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