http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 31 Aug 2018 at 15:01, Wahl, David M <dmw...@eagles.usi.edu> wrote: > > Hello GROMACS users, > > > I am attempting to run a molecular dynamics simulation with DNA complexed > with a small molecule. I have processed the molecule with ACPYPE, using the > GAFF, and merged the topology files into a single topology file. However, > when I attempt to use the “grompp” command before adding the ions with > genion, I get the following error: > > > Syntax error - File ligand_GMX.itp, line 3 Last line read: '[ atomtypes ]' > Invalid order for directive atomtypes > > > Originally in my single, merged topology file, I had the #include command for > the DNA chain topologies before the #include command for the ligand topology. > This is the order that resulted in the above error. > > > Whenever I moved the #include command for the ligand.itp file before the > #include command for the DNA chain .itp files, the error seemed to have gone > away. > > > Is this a valid fix for the syntax error? If it isn’t, do you have any > suggestions? If it is, why did it matter that the ligand was included before > the DNA? Under the [molecules] section I have DNA before the ligand so I’m > not understanding why it is the opposite for the #include commands? > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
