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 coordinate file does not match topology..." I should fix this one now!! Thanks a lot/Jamie
On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul <[email protected]> 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 <[email protected]<mailto: >> [email protected]>> 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 >> <[email protected] <mailto:[email protected]>> 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<[email protected] <mailto:[email protected]>> 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 >> <[email protected] <mailto:[email protected]>> 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 >> <[email protected] <mailto:[email protected]>> >> >> 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 [email protected] >> 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 [email protected]. >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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