[gmx-users] Water TIP4Pnew and topology file

Jennifer Vo quyviolet at gmail.com
Wed Apr 8 16:46:46 CEST 2015

Dear Experts,
I am dealing with this problem when trying to generate the .tpr file for
adding Ions for the system.
"number of coordinates in coordinate file (1zk3_solvate.gro, 159792) does
not match topology (topol.top, 208074)"

The system consits 4 chains of 4 proteins, 2 MG, uses Amber99SB ff and

The commands were:

pdb2gmx -f 1ZK3_ABCD.pdb -p 1zk3.top -o 1zk3.gro
editconf -f 1zk3.gro -o 1zk3_box.gro -bt cubic -d 1.2 -c
gmx solvate -cp 1zk3_box.gro -cs spc216.gro -o 1zk3_solvate.gro -p topol.top
grompp -f em_ion.mdp -c 1zk3_solvate.gro -p topol.top -o ions.tpr

When I do
cat 1zk3_solvate.gro | grep -c "OW"

 I have 48282 water molecules matching with topol.top file
SOL 48282

Do you have any idea for a solution?
Many thanks in advance.

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