Jamie, I asked you to show the order of sections ([defaults], [atomtypes], etc) as they go one after another after you added all the .itp files.
Now you gave me only the .top file file and I don't see what you have in the itp.'s. Please make a list of sections like [defaults], [atomtypes], [bonds], etc with respect to your .itp and look at the sequence. Something will not be correct here. Vitaly On Tue, Aug 11, 2009 at 12:46 AM, Jamie Seyed<jamie.se...@gmail.com> wrote: > Dear Vitaly, > topol.top: ------------- > #include "ffoplsaa.itp" > #include "spce.itp" > #include "c80ch3.itp" > [system] > fullerene in water > [molecules] > C80CH3 1 > SOL 1000 > -------------------- > my command is: > grompp -f md.mdp -c f.gro -p topol.top -o pr.tpr -maxwarn 10 > > Thank you for helping me out to solve the problem/ Regards/Jamie > > > On Mon, Aug 10, 2009 at 5:39 PM, Vitaly V. Chaban <vvcha...@gmail.com> > wrote: >> >> Jamie, >> >> The idea is the same. Some directive is not at its place. I cannot say >> which is exactly because I don't see all the picture with your >> topology file (+included files). Write the sequence of directives as >> they go in .top (+included .itp) and then we will see what sections >> must be shifted or maybe just swapped. >> >> Vitaly >> >> On Tue, Aug 11, 2009 at 12:34 AM, Jamie Seyed<jamie.se...@gmail.com> >> wrote: >> > Hi Vitaly, >> > When I add it back, I got the old error >> > ----------- >> > Program grompp, Version 4.0.5 >> > Source Code file: topio.c, line: 415 >> > Fatal error: >> > Syntax error-File ffoplsaa.itp, line 18 >> > last line read: >> > '[defaults]' >> > Invalid order for directive defaults >> > ----------- >> > Now do you have any idea??? I appreciate your help/Jamie >> > >> > On Mon, Aug 10, 2009 at 5:22 PM, Jamie Seyed <jamie.se...@gmail.com> >> > wrote: >> >> >> >> Hi Vitaly, >> >> I did it because I read from >> >> >> >> http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file >> >> that says: >> >> "One solution is to simply comment out (or delete) the lines of code >> >> out >> >> in the file where it is included for the second time i.e., ..". So if >> >> it is >> >> the case I am going to undo it to see what happens... I will let you >> >> know. >> >> Thanks/Jamie >> >> On Mon, Aug 10, 2009 at 5:05 PM, Vitaly V. Chaban <vvcha...@gmail.com> >> >> wrote: >> >>> >> >>> Why did you comment out [defaults] in ffoplsaa.itp? The general idea >> >>> is that the sections in the resulting topology file (after including >> >>> #include's) must be placed in the strict order. _______________________________________________ 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/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/mailing_lists/users.php