>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 <jsab...@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 :) > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
