Hi Justin, I used opls and I already tried PRODRG, but it did not help... I appreciate if you give the address of the related page of the website?? because I really problems to open some parts of the gromacs website. If non of them help, should I use molden myself to find all the entries??? Thank you very much for any suggestion.
On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jamie Seyed wrote: > >> 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. >> >> > > Depending on the force field you want to use, there are various scripts in > the User Contributions section of the Gromacs site. The PRODRG server is > also useful for generating an initial topology, but the charges and charge > groups it assigns are often unsatisfactory and require manual adjustment. > > -Justin > > Many Thanks in Advance, >> Jamie >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > -- > ======================================== > > 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 [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 >
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