The only thing antechamber uses QM for when it parameterizes compounds are
for the charge derivations. The fact that you are seeing 'bad'
conformations simply means that the force field parameters in gaff are
insufficient for your sugar, which is not surprising. The Woods group at
the University of Georgia has done a lot of good work on sugar force fields
(GLYCAM), so I suggest looking through some of the Amber documentation
(manuals) regarding Glycam and looking at some of their articles.
As is typically the case with force fields, it's critical that you get
torsion parameters properly fitted, and GAFF will almost certainly fail here
with many sugar torsions.
Hope this helps,
Jason
On Mon, Apr 4, 2011 at 9:05 PM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Dear Amber users,
> I have previously done QM/MM/MD simulation using AM1/OPLS potential for
> sugar substrate-enzyme complex. The sugar part was treated QM (AM1) while
> the rest of the system was treated MM. The MD results of such simulation
> showed that the sugar ring adopts 2,5B (boat) conformation during MD and
> that was with a perfect agreement with the crystal structure of the
> sugar-enzyme complex. This work was published..
> Recently, I am trying to do a different kind of calculations on the same
> system using Amber and I had to do two MD runs: one QM/MM (AM1 as well
> for
> the sugar part) and the other where I treated the whole system (sugar +
> enzyme) MM. The QM/MM results are pretty much as the one I done a while a
> go
> BUT the MM results showed a totally different conformation of the sugar
> ring
> even from the second picosecond of the simulation however I used
> antechamber
> to parametrize the sugar part using AM1 method then I expect that the
> sugar
> part behaves as if I treat it QM at AM1 but that did not work!
> I wonder, is there any way that I can make the sugar part under MM
> parameters behaves as if I treated it QM (AM1), can I do something like
> fitting parameters or so to avoid this unusual conformational behavior
> (which do not match with the crystal structure and reported studies)???
> Sharing ides/experience would be much appreciated
> Best wishes
> Mahmoud
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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 Mon Apr 04 2011 - 21:30:02 PDT
