On Sat, Aug 8, 2009 at 5:09 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Jamie Seyed wrote: > >> Hi Justin, >> I used opls and I already tried PRODRG, but it did not help... I >> > > What force field are you trying to use for your simulation? > I am using OPLS. > > > appreciate if you give the address of the related page of the website?? >> > > From the homepage: Downloads -> User Contributions -> Other software > Ok, Thanks > > > 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??? >> > > I don't know what you mean. However you assign parameters must be > consistent with the original derivation of the force field. Whether or not > you can do that in molden, I don't know. > > Between PRODRG and the contributed scripts, you should be able to write > toplogies for Gromos, OPLS, and AMBER. ok, I will try, Thanks. > > -Justin > > Thank you very much for any suggestion. >> >> On Sat, Aug 8, 2009 at 4:56 PM, Justin A. Lemkul <[email protected]<mailto: >> [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] >> <mailto:[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] >> <mailto:[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 <http://vt.edu/> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[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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