[gmx-users] Re: ions problem

[ahmet yıldırım]

problem solved:)

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
SOL               185
SOL               143
SOL             *33708*
NA                 *15*

16 Nisan 2011 21:22 tarihinde ahmet yıldırım <ahmedo047 at gmail.com> yazdı:

> Dear users,
>
> I am using gromacs 4.5.3. Initially I removed ligands from pdb file. Then
> I started to simulation .I met such a problem ( last error) after I added
> ions. What could be the problem?
> pdb2gmx -f withoutligand_xxx.pdb
> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
> *Fatal Error:*
> System has non-zero total charge: -1.500000e+01
>
> genion -s em.tpr -o solvated.gro -pname NA+ -np 15 -g em.log
> select: Group 13 (SOL)
> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> *Fatal error:*
> number of coordinates in coordinate file (solvated.gro, 106473)
> does not match topology (topol.top, 106518)
>
> *topol.top:*
> ..
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> SOL                   185
> SOL                   143
> SOL                33723
> NA                       15
>
> --
> Ahmet YILDIRIM
>



-- 
Ahmet YILDIRIM
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