Quoting minnale <[EMAIL PROTECTED]>: > > > Thanks Justin for your reply, > May be this is a trivial question, That procedure can follow who wants to use > opls-aa ff with lipids?
Yes, describe the protein with OPLS-AA and follow the procedure to make lipid.itp compatible with OPLS-AA. The parameters for the lipids are still the so-called "Berger lipids," which I believe were originally based off of OPLS-AA parameters. -Justin > > On Fri, 25 Apr 2008 Justin A.Lemkul wrote : > >Quoting minnale <[EMAIL PROTECTED]>: > > > > > > > > Thanks Mark for your reply, > > > I wanted to ask you that, the link which I mentioned means opls-aa ff > > > specifially for lipids? > > > I wanted to use opls-ff for both protein and lipid , shall I follow the > > > procedure according to the link. > > > http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html > > > Thanks for your invaulable suggestion. > > > >The procedure Chris posted at that link is so that one can use the Berger > lipid > >parameters (available at Tieleman's site) compatible with OPLS-AA, which is > >used for the protein. Follow what he says in that message closely; there > have > >also been more recent discussions about using that particular procedure if > you > >have other questions or run into difficulty. > > > >-Justin > > > > > >======================================== > > > >Justin A. Lemkul > >Graduate Research Assistant > >Department of Biochemistry > >Virginia Tech > >Blacksburg, VA > >[EMAIL PROTECTED] | (540) 231-9080 > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > >======================================== > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.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
