Xleap's editor is actually useful for cleanup of structures by
successively selecting, dragging, and minimizing.
Bill
Jason Swails <jason.swails.gmail.com> wrote:
> The barrier to getting "unstuck" is too high, I guess. You could try some
> simulated annealing or something like that...
>
> But fixing the initial structure is still the better approach, IMO.
>
> Good luck,
> Jason
>
> On Tue, Feb 26, 2013 at 3:19 PM, Jio M <jiomm.yahoo.com> wrote:
>
> > Dear Lachele and Jason;
> >
> > Thanks for explanation and suggesting impose command (Jason also
> > suggested).
> > Just for knowledge sake I was curious why MD run couldn't resolve this
> > issue (if fragments remain stuck inside rings even after minimization they
> > keep stuck during MD run!)
> >
> > thanks,
> >
> >
> >
> >
> > ________________________________
> > From: Lachele Foley <lf.list.gmail.com>
> > To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> > Sent: Tuesday, February 26, 2013 10:02 PM
> > Subject: Re: [AMBER] adding rings using sequence command
> >
> > Minimization will only find the lowest local energy minimum using only
> > very local knowledge of forces. So, it has no good way of resolving
> > an issue like that. In general, it will take less energy to expand
> > all bonds in a ring slightly, and leave a branch intruding, than to
> > greatly stretch one bond in the ring to allow the branch to escape.
> >
> > We see this frequently, and are developing tools for automating
> > resolution. But, that might take a while. In the meantime, you have
> > to fix it yourself.
> >
> > When you have those situations, it is best to resolve them before
> > minimization. Of course, you might use a brief minimization to
> > determine if you have a problem, then go back and fix the
> > pre-minimized structure. Use the impose command in tleap to alter
> > angles. Altering angles far from the intrusion site will require the
> > least change in any given angle. The AmberTools12 manual contains a
> > good description of the command, and there are additional examples in
> > the section on building oligosaccharides.
> >
> >
> > On Tue, Feb 26, 2013 at 2:49 PM, Jio M <jiomm.yahoo.com> wrote:
> > > Dear Jason,
> > >
> > >
> > > Thanks for the suggestions. But please clarify this also (and correct
> > me):
> > > By mistake (which I realized after MD run) I had used the same structure
> > in which many rings were crossed by polymer chain fragments and run
> > minimization and later MD for 10 ns. I think such criss cross from rings
> > should have been removed by doing this, but it did not help.
> > >
> > > On the contrary if we run some simulation we never see branches crossing
> > the rings; I mean I never saw the "bonds" of fragments (which are just
> > bonds by distance) crossing the rings. So I think its vdw radii which
> > prevents this. I was wondering why after running minimization and later MD
> > did not resolve this issue and the polymer fragments remained stuck inside
> > the rings?
> > >
> > > regards,
> > >
> > > Jiomm
> > >
> > >
> > > ________________________________
> > > From: Jason Swails <jason.swails.gmail.com>
> > > To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> > > Sent: Tuesday, February 26, 2013 5:53 PM
> > > Subject: Re: [AMBER] adding rings using sequence command
> > >
> > > On Tue, Feb 26, 2013 at 9:55 AM, Jio M <jiomm.yahoo.com> wrote:
> > >
> > >> Hi All,
> > >>
> > >> I am working on some polymeric system and want to introduce naphthalene
> > >> like ring system in polymer at intervals. I am using sequence command to
> > >> add ring residues to the polymer. As polymer is a complex system so
> > when I
> > >> add a ring residues at intervals of polymer using sequence command few
> > >> rings are added in such a manner that some polymer fragments criss cross
> > >> the ring. Its not a good idea to somehow relax the rings using xleap
> > one by
> > >> one as there are many ring systems.
> > >>
> > >
> > > Maybe try changing your residue template for your polymer building
> > block...
> > > The tleap sequence functionality is very simplistic (and therefore
> > limited)
> > > -- you can look into some of the commands to adjust structure (like
> > > 'impose', I believe) -- the GLYCAM folks have done some very clever
> > things
> > > getting tleap to build carbohydrates, but it is not easy (at least it's
> > not
> > > easy for me).
> > >
> > > You may be better off trying to build your structure elsewhere (or put a
> > > good deal of effort into learning how to 'really' use tleap).
> > >
> > > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Feb 26 2013 - 23:30:02 PST
