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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Received on Mon Apr 04 2011 - 21:00:03 PDT
