[gmx-users] Model of water

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Oct 6 16:32:29 CEST 2012

I did as follow as I described, but there is an error:
1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic
2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top

Then added #include "charmm36.ff/tip3p.itp" to topol.top

3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr
Fatal error:
number of coordinates in coordinate file (popc-solv.gro, 74672)
             does not match topology (topol.top, 104936)
I checked the water molecules of popc-solv.gro by grep command ;

# grep -c HW popc-solv.gro

[ molecules ]
; Compound        #mols
POPC              238
SOL             24348

What is the problem? would you please help me? I think the SOL molecule are counted twice!!

Thanks in advance.

----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, October 6, 2012 4:44 PM
Subject: Re: [gmx-users] Model of water

On 10/6/12 8:59 AM, Shima Arasteh wrote:
> To use tip3p water model, I copied popc.top and popc.itp in my working directory. I removed the line of #include tips3p from top file. Also removed SOL in moleculetypes.
> Then I ran genbox :
> #genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top
> genbox added SOL but there is not any water model including in my top file, so I added #include "charmm36.ff/tip3p.itp" to top file manually:
> Next, I ran energy minimization. Is my procedure correct? How would I be sure that " tip3p " is used as water model?

Your approach is correct.  genbox will not write topology information (i.e. 
#include statements) to your topology for you.  It adds coordinates to your 
configuration and updates the [molecules] section, nothing more.  It is up to 
you to tell grompp what parameters to apply to the water molecules.

If your topology #includes a TIP3P topology, that's what grompp will use.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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