Hi
ntr=1, restraintmask="!:7" restraint_wt=(whatever you want)
this will restrain everybody except residue 7
On Fri, Mar 12, 2010 at 12:25 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> I've also copied this to the mailing list, which is where all replies
> to such threads should be sent. You can use ntr=1 and set a restraint
> weight and a restraint mask that selects all protein residues. This
> should have the effect you're looking for. These features are
> well-documented in the manual.
>
> Good luck!
> Jason
>
> On Fri, Mar 12, 2010 at 10:42 AM, rui <ruisher.gmail.com> wrote:
> > Hi, Jason,
> >
> > Thanks for your reply. When I try to minimize the structure, is there
> anyway
> > that I can keep the protein frozen and only minimize the ligand and the
> > covalent bonded residues? Looks like my structure change a lot (RMSD 2A),
> > and I'm wondering if I can fix some part of it. Thanks.
> >
> > On Tue, Mar 9, 2010 at 2:01 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> On Tue, Mar 9, 2010 at 1:37 PM, rui <ruisher.gmail.com> wrote:
> >> > Hi, All,
> >> >
> >> > I need to calculate/minimize the energy for a protein ligand complex,
> >> > the
> >> > protein and the ligand is covalently bonded, is amber able to handle
> >> > this
> >> > problem? If so, can anyone suggest how to do it? Thanks.
> >>
> >> A covalently bound "ligand" is treated no differently than any other
> >> amino acid residue in a protein. The manual and tutorial page (
> >> www.ambermd.org/tutorials ) give a good introduction on using Amber.
> >>
> >> Good luck!
> >> Jason
> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> ---------------------------------------
> >> Jason M. Swails
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-4032
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Fri Mar 12 2010 - 14:00:03 PST
