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.
On Mon, Aug 10, 2009 at 11:50 PM, Jamie Seyed<[email protected]> wrote: > Hi Vitaly, > Thanks for your good comments. Yes I deleted that and I run the program but > finally I found a line that said 26 inconsistent shifts.... > So I tried to do everything again properly. Now I faced with several > problems and to get rid of them: > I put ff*.itp in the top line of topol.top, I commented out the line > [defaults] in ffoplsaa.itp > but now I have a new error that > ----------------------------- > Fatal error: syntax eror -File ffoplsaanb.itp, line 1 > last line read: > '[atomtype]' > Invalid order for directive atomtype > ---------------------------- > I did not mixed the ff and I put ff.itp on the top of my topology file... > would you please let me know what is causing the problem?? I appreciate your > help.../Jamie > > On Mon, Aug 10, 2009 at 4:29 PM, Vitaly V. Chaban <[email protected]> > wrote: >> >> Dear Jamie, >> >> > 1) when I have my itp file and only I need a gro file (with velocities) >> > how >> > can I make it?? >> .gro can be made from .pdb with editconf. Also you will find useful >> genbox and genconf for the related tasks. The velocities are not >> needed to start MD run. They can be assigned automatically by mdrun >> with "gen_vel" keyword in grompp.mdp. >> >> > 2) with Christopher Stiles method, why I got that fatal error and how I >> > can >> > solve it to run a correct md simulation?? >> What is the group BAL in your system? I guess you mentioned it in the >> .mdp file, so the program looks for it and doesn't find anywhere. >> Either delete it from .mdp or provide an information which atoms this >> group contains (see "-n index.ndx"). >> >> Good luck, >> Vitaly >> >> On Mon, Aug 10, 2009 at 9:53 PM, Jamie Seyed<[email protected]> wrote: >> > Dear Vitaly and all, >> > I did copy my top file to a itp file and now for doing a md simulation I >> > need a box of water and so I was thinking to make a .gro file and use >> > editconf after that. But I did not know how, so I used the procedure by >> > Christopher Stiles (I used editconf to make a gro file from pdb and I >> > did >> > not use my itp according to the procedure....) the gro file doesn't >> > contain >> > velocities. Now when I run the grompp command, I got this Fatal error: >> > Group BAL not found in indexfile.... >> > my questions are >> > 1) when I have my itp file and only I need a gro file (with velocities) >> > how >> > can I make it?? >> > 2) with Christopher Stiles method, why I got that fatal error and how I >> > can >> > solve it to run a correct md simulation?? >> > Many Thanks in advance/Jamie >> > >> > On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban <[email protected]> >> > wrote: >> >> >> >> Jamie, >> >> >> >> The best solution is to copy all the sections ([atoms], [bonds], etc) >> >> corresponding to each molecule into a separate file and then use >> >> "include" statement like in C language to attach these .itp files to >> >> .top file. >> >> >> >> So you will have only the numbers of the each kind of molecules in >> >> your .top file. These manipulations are made only in the sake of >> >> future comfort. Below is an example how I do it. >> >> >> >> Best, >> >> Vitaly >> >> >> >> ===============topology file============== >> >> #include "vvc.itp" >> >> #include "15x15x50.itp" >> >> #include "20x20x50.itp" >> >> #include "25x25x50.itp" >> >> >> >> >> >> [ system ] >> >> MWCNT with LIBF4 solution >> >> >> >> >> >> [ molecules ] >> >> 15x15x50 1 >> >> 20x20x50 1 >> >> 25x25x50 1 >> >> LI+ 7 >> >> BF4 7 >> >> Methanol 254 >> >> >> >> >> >> On Mon, Aug 10, 2009 at 4:38 PM, Jamie Seyed<[email protected]> >> >> wrote: >> >> > Dear Vitaly, >> >> > Thanks for your reply. Justin helped me about that and I could get >> >> > the >> >> > topology by x2top. In your last email you said after that I can >> >> > export >> >> > it to >> >> > the .itp right? Would you please explain more about that, I mean for >> >> > example >> >> > should I change it manually to be look like a itp file or is that >> >> > something >> >> > else?? I appreciate your help... >> >> > Thanks a lot/Jamie >> >> > >> >> > On Mon, Aug 10, 2009 at 2:18 AM, Vitaly V. Chaban >> >> > <[email protected]> >> >> > wrote: >> >> >> >> >> >> Jamie, >> >> >> >> >> >> What error messages do they provide? What force fields do you use? >> >> >> There were many rumors about these utilities here in the list but >> >> >> they >> >> >> seem to be workable in most cases. >> >> >> >> >> >> Vitaly >> >> >> >> >> >> On Mon, Aug 10, 2009 at 1:39 AM, Jamie Seyed<[email protected]> >> >> >> wrote: >> >> >> > Hi Vitaly, >> >> >> > Actually it doe's not work. I tried but I got error messages for >> >> >> > both >> >> >> > cases. >> >> >> > Actually the structure is big and contains a c60 part. Do you have >> >> >> > any >> >> >> > advice? I could not find in the topology part of archive... >> >> >> > Thanks/Jamie >> >> >> > >> >> >> > >> >> >> > On Sun, Aug 9, 2009 at 2:54 AM, Vitaly V. Chaban >> >> >> > <[email protected]> >> >> >> > wrote: >> >> >> >> >> >> >> >> Hi, >> >> >> >> >> >> >> >> Did you try pdb2gmx, x2top to make .top and then export to .itp? >> >> >> >> Sometimes also it appears easier to make the topology by hand if >> >> >> >> your >> >> >> >> structure is not big. Please see the topologies for some >> >> >> >> molecules >> >> >> >> in >> >> >> >> the gromacs archive to use them as an example. >> >> >> >> >> >> >> >> Vitaly >> >> >> >> >> >> >> >> > >> >> >> >> > Dear gmx users, >> >> >> >> > I need some help for generating a itp file for my molecular >> >> >> >> > structure. I >> >> >> >> > am >> >> >> >> > using molden and now I have the xyz and pdb files. I read >> >> >> >> > through >> >> >> >> > mailing >> >> >> >> > list but seems I should provide itp myself. But I don't know >> >> >> >> > the >> >> >> >> > right >> >> >> >> > way >> >> >> >> > to do that. Is it using molden and find one-by-one bond sand >> >> >> >> > angles >> >> >> >> > and >> >> >> >> > dihedrals... . If I have already the itp file for a part of >> >> >> >> > molecule >> >> >> >> > is >> >> >> >> > it >> >> >> >> > only to add the information of new atoms to the old itp file?? >> >> >> >> > I >> >> >> >> > will >> >> >> >> > really >> >> >> >> > appreciate it if someone gives me better ideas and more related >> >> >> >> > information >> >> >> >> > to make my itp file. >> >> >> >> > >> >> >> >> > Many Thanks in Advance, >> >> >> >> > Jamie >> >> >> >> > -------------- next part -------------- >> >> >> >> > An HTML attachment was scrubbed... >> >> >> >> > URL: >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > http://lists.gromacs.org/pipermail/gmx-users/attachments/20090808/aaef0139/attachment-0001.html >> >> >> >> _______________________________________________ >> >> >> >> 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 >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Vitaly V. Chaban, Ph.D. (ABD) >> >> >> School of Chemistry >> >> >> V.N. Karazin Kharkiv National University >> >> >> Svoboda sq.,4, Kharkiv 61077, Ukraine >> >> >> email: [email protected],[email protected] >> >> >> skype: vvchaban, cell.: +38-097-8259698 >> >> >> http://www-rmn.univer.kharkov.ua/chaban.html >> >> >> =================================== >> >> >> !!! Looking for a postdoctoral position !!! >> >> >> =================================== >> >> > >> >> > >> > >> > >> >> >> >> -- >> Vitaly V. Chaban, Ph.D. (ABD) >> School of Chemistry >> V.N. Karazin Kharkiv National University >> Svoboda sq.,4, Kharkiv 61077, Ukraine >> email: [email protected],[email protected] >> skype: vvchaban, cell.: +38-097-8259698 >> http://www-rmn.univer.kharkov.ua/chaban.html >> =================================== >> !!! Looking for a postdoctoral position !!! >> =================================== > > -- Vitaly V. Chaban, Ph.D. (ABD) School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: [email protected],[email protected] skype: vvchaban, cell.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html =================================== !!! Looking for a postdoctoral position !!! =================================== _______________________________________________ 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
