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 <vvcha...@gmail.com>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<jamie.se...@gmail.com> 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 <vvcha...@gmail.com> > > 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<jamie.se...@gmail.com> > 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 <vvcha...@gmail.com> > >> > 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 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 > >> > > >> > > >> > >> > >> > >> -- > >> Vitaly V. Chaban, Ph.D. (ABD) > >> School of Chemistry > >> V.N. Karazin Kharkiv National University > >> Svoboda sq.,4, Kharkiv 61077, Ukraine > >> email: cha...@univer.kharkov.ua,vvcha...@gmail.com > >> skype: vvchaban, cell.: +38-097-8259698 > >> http://www-rmn.univer.kharkov.ua/chaban.html > >> =================================== > >> !!! Looking for a postdoctoral position !!! > >> =================================== > > > > >
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