Dear, I created a 5 5 2 box containing 15 mibc and 15 decanol molecues by using two comands: *genbox -ci decanol.gro -nmol 15 -box 5 5 2 -o layer.gro -p decanol.top genbox -cp layer.gro -ci decanol.gro -nmol 15 -box 5 5 2 -o box.gro -p mibc.top* then I filled this mixture by water to create other 5 5 10 box by using comands: *genbox -cp mix.gro -cs spc216.gro -o box1.g96 -p topol.top -box 5 5 10*
the topol.top file is: *#include "ffG43a1.itp" #include "decanol.itp" #include "mibc.itp" ; include water #include "spce.itp" [ system ] MIBC and dec in water [ molecules ] dec 15 mibc 15 sol 7947.* then I ran the grompp comand: grompp -f input_min.mdp -o min.tpr -c box1.g96 and the errors was *Warning: atom name 2 in topol.top and box1.g96 does not match (CAC - CAF)* *Warning: atom name 3 in topol.top and box1.g96 does not match (CAE - CAB)* *Warning: atom name 4 in topol.top and box1.g96 does not match (CAG - CAE)* *Warning: atom name 5 in topol.top and box1.g96 does not match (CAI - CAG)* *Warning: atom name 6 in topol.top and box1.g96 does not match (CAK - CAC)* *Warning: atom name 7 in topol.top and box1.g96 does not match (CAJ - OAD)* *Warning: atom name 8 in topol.top and box1.g96 does not match (CAH - HAN)* *Warning: atom name 9 in topol.top and box1.g96 does not match (CAF - CAA)* *Warning: atom name 10 in topol.top and box1.g96 does not match (CAD - CAF)* *WARNING 1 [file topol.top, line 20]:* * 220 non-matching atom names* * atom names from topol.top will be used* * atom names from box1.g96 will be ignored* *--------------------------------------------------- * *Fatal error:* *Too many warnings (2), grompp terminated.* *If you are sure all warnings are harmless, use the -maxwarn option.* *For more information and tips for troubleshooting, please check the GROMACS * *website at http://www.gromacs.org/Documentation/Errors * Please help me to correct these errors. Thank you very much best regards, Cuong 2011/11/7 Justin A. Lemkul <jalem...@vt.edu> > > > cuong nguyen wrote: > >> Dear, >> >> Thanks a lot Justin. I created a box containing mixed solution of 20 >> hexanol molecues and 20 octanol molecules in water. However, when I run >> grompp and mdrun commands, gromacs noticed errors with the topol.top file >> for this mixed system. >> >> So please help me to create a suitable topol.top file to this system. >> >> > No one can help you without knowing the exact errors that grompp produced. > > -Justin > > Thanks a lot. >> >> Best regards, >> >> >> Cuong >> >> 2011/11/7 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> >> >> Justin A. Lemkul wrote: >> >> >> >> cuong nguyen wrote: >> >> Dear, >> >> I would like to create a solution of mix substances (hexanol >> and octanol) in water. I got top files and gro files of >> these alcohols from PRODRG server. However I do not know how >> to mix these top file to create topol.top file for this >> mixture. >> >> >> Please read the tutorial: >> >> http://www.gromacs.org/__**Documentation/Tutorials#__** >> Heterogeneous_Systems<http://www.gromacs.org/__Documentation/Tutorials#__Heterogeneous_Systems> >> >> <http://www.gromacs.org/**Documentation/Tutorials#** >> Heterogeneous_Systems<http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems> >> > >> >> >> Also possibly useful: >> >> >> http://www.gromacs.org/__**Documentation/How-tos/Mixed___**Solvents<http://www.gromacs.org/__Documentation/How-tos/Mixed___Solvents> >> >> <http://www.gromacs.org/**Documentation/How-tos/Mixed_**Solvents<http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents> >> > >> >> -Justin >> >> >> -- ==============================**__========== >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> -- >> Nguyen Van Cuong >> PhD student - Curtin University of Technology >> Mobile: (+61) 452213981 >> >> > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981
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