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-us...@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 !!! =================================== _______________________________________________ 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
