[gmx-users] Water TIP4Pnew and topology file

[Smith, Micholas D.]

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
TIP4Pnew.

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.
Regards,
Jennifer
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