Dear Dallas the command are: FOR PVDF gmx x2top -f PVDF_chain.gro -o PVDF_chain.top -ff oplsaa -name
the system gives me this lines: Opening force field file /usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomname2type.n2t There are 23 names to type translations in file oplsaa.ff Generating bonds from distances... atom 44 Can not find forcefield for atom C21-2 with 3 bonds Can not find forcefield for atom C18-5 with 3 bonds Can not find forcefield for atom C16-10 with 3 bonds etc etc Fatal error: Could only find a forcefield type for 302 out of 602 atoms The same thing happens with graphene oxide. The problem is that I built in the past combined systems of these two molecules, without problems. I created an executable n2t file as I mentioned in the previous post. Maria Luisa Thank you for your help > Sorry, can't help you directly, but can you post some of the commands > that you've actually run (copy and paste the exact lines), then the > error messages that you get (again a direct copy and past). Be as > specific as you can be, including the different things you have > attempted to use, and the results. > > The more exact details you give, the more able people are to help. > > 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 Wed, 3 Oct 2018 at 19:32, Maria Luisa <ml.perro...@itm.cnr.it> wrote: >> >> Dear users, >> I need help. I want to build the topology of a polymeric chain of PVDF >> of >> 602 atoms, and of a sheet of Graphene Oxide of 202 atoms. I use the >> version of gromacs 5.1.4. The problem is that it does not recognize some >> atoms in the polymeric chain, and not at all the graphene oxide atoms. I >> already worked with the x2top command, I had already created another >> executable .n2t file, to complete the missing atoms in the atomname >> file, >> and in the past I built topology for graphene oxide and graphene >> systems, >> but now, all this command with my previous challenge doesn't t work. I'm >> doing a thousand tests but I do not know how to do it. >> >> I hope to get help. >> Thank you >> >> Maria Luisa Perrotta >> Ph.D Student, CNR-ITM >> via P.Bucci, 87036 Rende (Cs) >> Italy >> email: ml.perro...@itm.cnr.it >> >> >> -- >> 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. > Maria Luisa Perrotta Ph.D Student, CNR-ITM via P.Bucci, 87036 Rende (Cs) Italy email: ml.perro...@itm.cnr.it -- 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.