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
>
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 26 2013 - 12:30:06 PST
