[gmx-users] Water TIP4Pnew and topology file

[Jennifer Vo]

Dear Micholas ,
Many thanks for your recommendation. I have found the solution by replacing
spc216.gro  by tip4p.gro in gmx solvate.
Regards,
Jennifer

On Wed, Apr 8, 2015 at 5:04 PM, Smith, Micholas D. <smithmd at ornl.gov> wrote:

> 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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