To simplify finding the problems, you might consider doing a
minimization. Minimizations are cheap and fast. If the minimization
works, and the resulting structure is sound, then proceed. If there
are troubles, the minimization will generally show you just where they
are.
We will gladly add your structure to our list of test cases, if you
like. We would have this done already if we had enough people around
to do it!
On Wed, Feb 27, 2013 at 4:52 AM, Jio M <jiomm.yahoo.com> wrote:
> Dear Bill Ross,
>
> Thanks for suggestion but I have many such anomalies in my system (number of rings crossed by fragments). So doing it manually and looking for crossed rings (which can be missed if done with manual eyes) will be like searching needle in a haystack :-)
> P.S.:
> I am looking for some automated way of doing this. I think as Lachele said they are implementing few such things and developing tools, if someone from AMBER is interested (may be personal mail discussion I can share my structure;; ahem! little bold) we can implement few things automatically as a ''general purpose tool'' (scripting, programing; I write perl) to solve this as I need few suggestions regarding internal frame work especially of tleap/xleap modules and other modules of AMBER helping in building or generating molecules.
>
> regards,
>
>
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.EDU>
> To: amber.ambermd.org
> Sent: Wednesday, February 27, 2013 9:00 AM
> Subject: Re: [AMBER] adding rings using sequence command
>
> 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
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Feb 27 2013 - 13:00:02 PST
