[gmx-users] No such moleculetype SOL

Mark Abraham mark.j.abraham at gmail.com
Sat Sep 21 21:41:55 CEST 2013

On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury <jsabou1 at gmail.com> wrote:
> I am doing this tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
> I have set up the randomly placed cyclohexane and water throughout the box.
> The problem is when i try the command "grompp -f em.mdp -c biphase.gro -p
> cyclohexane.top -o em.tpr" it errors telling me "No such moleculetype SOL".
> I know SOL is water, and the .top file does not include any sort of .itp
> that includes water.

Have a look at how Justin's tutorial's .top gets access to a water topology.


> I've tried to add "#include
> "amber99sb.ff/forcefield.itp"" with no avail.
> This is strictly just cyclohexane and water, I am not interested in putting
> a protein inside of it.
> Commands used: http://pastebin.com/raw.php?i=RaKNCpi4
> Files: http://www.sendspace.com/file/ibwk3l
> Thank you, the help you guys give is extremely appreciated :)
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