Dear users, I was mentioning about OPLSAA force field for ATP and other small molecule. I just wanted to know the procedure to be followed and some guidance from people who have created topologies for such molecules manually. I am going through chapter 5 of the manual. But wanted some useful suggestions.
Thank you With Regards M. Kavyashree On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Kavyashree M wrote: > >> Dear gromacs users, >> >> I wanted to know the steps to be followed >> in order to generate a topology for a new >> ligand. I went through the mailing list and >> http://www.gromacs.org/**Documentation/How-tos/**Parameterization<http://www.gromacs.org/Documentation/How-tos/Parameterization> >> but was not clear. >> >> > All force fields are different, and since you haven't said which one you're > trying to use there's nothing that anyone can tell you. Read the primary > literature for the force field you want to use and follow the procedure laid > out therein. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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