[gmx-users] Re: No such moleculetype SOL

[Jonathan Saboury]

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

Thank you very much for the response Mark!

I've looked at his .top and it seems to me that how he included it is by
adding "#include spc.itp". I've added that line to cyclohexane.top before
and after the "#include "cyclohexane.itp" with no success (same error as
before).

I also saw that he added a force field. Would I need to do this if I am not
interested in a protein?

I want to avoid using PRODRG because it is online which admins can easy see
what I uploaded. I feel much more comfortable using programs on my system
(the reason I am using acpype).

Thanks again :)

- Jonathan Saboury






On Sat, Sep 21, 2013 at 12:06 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. 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 :)
>