Dear all, I have a topology contains line as below. I do not understand what is wrong with it that I get an 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 -------------- according to the page http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file I do not have twice default section... SO I do not know exactly which files I should check... It says topology and ff. Topology that I am using in grompp is as below and the ffoplsaa.itp has only one default section... Would you please help me to solve the problem. topol.top: ------------- #include "ffoplsaa.itp" #include "spce.itp" #include "molecule.itp" [system] fullerene in water [molecules] molecule 1 SOL 1000 -------------------- Many Thanks in Advance and I appreciate your help/Jamie
On Mon, Aug 10, 2009 at 5:46 PM, 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. >> > >
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