Hi Justin, Ok.Thanks for comments and advice, I appreciate.../Jamie On Mon, Aug 10, 2009 at 3:06 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Jamie Seyed 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 >> > > The .gro file will not contain velocities until you have run dynamics. > > error: >> Group BAL not found in indexfile.... >> > > Then you have specified a molecule type that is not encompassed by your > #included .itp files, or you have specified some special group in your .mdp > file that doesn't exist without using a special index group. > > my questions are >> 1) when I have my itp file and only I need a gro file (with velocities) >> how can I make it?? >> > > I don't understand this question. > > 2) with Christopher Stiles method, why I got that fatal error and how I can >> solve it to run a correct md simulation?? >> > > See above. Without seeing the topology and .mdp file, it is hard to > provide any more useful advice. > > I would seriously recommend running some simple tutorials on proteins (even > if you don't care about proteins - these systems are very robust) to get a > feel for procedures in Gromacs, how velocities are generated, how to use > index files (if necessary), etc. > > -Justin > > Many Thanks in advance/Jamie >> >> On Mon, Aug 10, 2009 at 10:45 AM, Vitaly V. Chaban >> <vvcha...@gmail.com<mailto: >> 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 >> <mailto: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 <mailto: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 <mailto: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 <mailto: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 >> <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>. >> >> >> 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 >> <mailto:cha...@univer.kharkov.ua>,vvcha...@gmail.com >> <mailto:vvcha...@gmail.com> >> >> skype: vvchaban, cell.: +38-097-8259698 >> >> http://www-rmn.univer.kharkov.ua/chaban.html >> >> =================================== >> >> !!! Looking for a postdoctoral position !!! >> >> =================================== >> > >> > >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > 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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