[gmx-users] Re:Understanding about OPLS-aa lipids
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 25 14:07:57 CEST 2008
Quoting minnale <minnale_gnos at rediffmail.com>:
> 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
> On Fri, 25 Apr 2008 Justin A.Lemkul wrote :
> >Quoting minnale <minnale_gnos at rediffmail.com>:
> > >
> > > 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
> >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
> >also been more recent discussions about using that particular procedure if
> >have other questions or run into difficulty.
> >Justin A. Lemkul
> >Graduate Research Assistant
> >Department of Biochemistry
> >Virginia Tech
> >Blacksburg, VA
> >jalemkul at vt.edu | (540) 231-9080
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul at vt.edu | (540) 231-9080
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