[gmx-users] ions problem

ahmet yıldırım ahmedo047 at gmail.com
Sat Apr 16 20:22:59 CEST 2011

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)

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
SOL                   185
SOL                   143
SOL                33723
NA                       15

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