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
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Feb 26 2013 - 12:30:03 PST
