[AMBER] cis form: avoiding atom overlap in all-atom modeling

From: bio lab <biolabcs.gmail.com>
Date: Thu, 18 Oct 2012 18:42:13 +0200

Dear Amber community members,



I would like to know your opinion whether it is possible or not to observe
a trans-to-cis transition of Resveratrol in MD simulation by using the
GAFF/Amber force-field. This molecule is present in nature in both forms
(and the cis form is also more stable), as it can be seen on the following
Wikipedia image:



http://en.wikipedia.org/wiki/File:Cis_and_trans_resveratrol.PNG



In the cis form the two 6-atom rings are very close. It seems to me that
the H atoms that are attached to the two closest C atoms would overlap when
modeled with an all-atom force-field like Amber, thus inhibiting the
possibility of obtaining the cis form. Indeed, in MD simulation I observe
many (short-lived and incomplete) rotations of the corresponding dihedral
angle: they are sufficiently large to overcome the energy barrier (<90),
but the molecule always returns back to the trans form (180) and never
ends up in the cis one (0).



Therefore, my question is the following: is it possible to observe this in
MD simulation? Or does it require any kind of special modeling of the
molecule, for instance the two 6-atom rings cannot be considered planar in
the cis form? Or should I try in this case a united-atom force-field?



Thanks in advance for any comment or suggestion.
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Received on Thu Oct 18 2012 - 10:00:04 PDT
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