First I put 1000, but after editconf and genbox it has been changed to 572. I only have 1 part with SOL 572...
On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Jamie Seyed wrote: > >> Hi Justin, >> Thanks again... . Actully I have a question: I have 1836 atoms (572 water >> and 1 molecule with 120 atoms). In top of my file.gro I have 1836 and in >> topology in [molecules] I have c60ch3 1; and SOL 572 which means the same as >> above. So how I should change it to get rid of error...??/ >> > > The above should be correct. However, you then have in your .top you > posted earlier: > > [molecules] > molecule 1 > SOL 1000 > > This section is probably the source of your problem. Again, as I said > before, there should only ever be one [ molecules ] section in the .top > file. Sounds like you've got two. > > -Justin > > Thank you in advance.../Jamie >> On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Jamie Seyed wrote: >> >> Hi Justin, >> Oh yes. I had a line that include ff again and I deleted that >> (is that ok)? now I got a new error related to "number of >> coordinates in >> >> >> That's more than OK, that's correct. As Mark pointed out, there >> should only ever be one invocation of [ defaults ] in a topology. >> >> >> coordinate file does not match topology..." I should fix this >> one now!! >> >> Simple one to fix. Figure out where the duplicate or missing >> molecules are within the topology. I'm guessing your molecule.itp >> was really a molecule.top, complete with [ defaults ], [ system ], >> and [ molecules ] directive, right? None of these should be present >> in an .itp file, only a .top. >> >> -Justin >> >> Thanks a lot/Jamie >> >> >> On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> Can you post the contents of molecule.itp? The first >> #include for >> the force field is likely not the problem; you've probably >> #included >> it again in molecule.itp. >> >> -Justin >> >> Jamie Seyed wrote: >> >> 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 <mailto:jamie.se...@gmail.com> >> <mailto:jamie.se...@gmail.com <mailto:jamie.se...@gmail.com>> >> <mailto:jamie.se...@gmail.com >> <mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com >> <mailto: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 <mailto:vvcha...@gmail.com> >> <mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>> >> <mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com> >> <mailto:vvcha...@gmail.com <mailto: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 >> <mailto:jamie.se...@gmail.com> >> <mailto:jamie.se...@gmail.com >> <mailto:jamie.se...@gmail.com>> <mailto:jamie.se...@gmail.com >> <mailto:jamie.se...@gmail.com> >> >> <mailto:jamie.se...@gmail.com >> <mailto: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 >> <mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com >> <mailto:jamie.se...@gmail.com>> >> <mailto:jamie.se...@gmail.com >> <mailto:jamie.se...@gmail.com> <mailto:jamie.se...@gmail.com >> <mailto: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 <mailto:vvcha...@gmail.com> >> <mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com>> >> <mailto:vvcha...@gmail.com <mailto:vvcha...@gmail.com> >> <mailto:vvcha...@gmail.com <mailto: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 >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > 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 >
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