[gmx-users] Water TIP4Pnew and topology file

Smith, Micholas D. smithmd at ornl.gov
Wed Apr 8 17:04:47 CEST 2015

How many ions did you add?

You need to include in your .top file (after SOL) a line for each Ion type and the number of them. This needs to sum to 208074.

Also make sure Ions.itp is included in your .top file

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Jennifer Vo <quyviolet at gmail.com>
Sent: Wednesday, April 08, 2015 10:46 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Water TIP4Pnew and topology file

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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