[AMBER] RED: Charge derivation of transtion state analogue

From: manoj singh <mks.amber.gmail.com>
Date: Sun, 5 Jul 2009 07:10:57 +0100

Dear Amber Users,
I am trying to study binding properties of one substrate and
its transition state analogue in Amber10.

I derived charges of the substrate in RED-III, using its single orientation
and single conformation.

For transition state analogue I have change the bond length of partial
breaking bonds and constraint the partial formed bond distance using
distance based restrain, consistence to the previous quantum study for the
reaction mechanism (method is similar to Angw. Chem. Int. Ed. Volume 45
Issue 4 <http://www3.interscience.wiley.com/journal/112226663/issue>,
Pages 653 - 657,
used with other system). I ran the molecular dynamics of the this system
to equilibrate the structure according to the new bond lengths at reaction
center. Now, I want to fit the charges of substrate, water molecule and the
amino acids taking part in reaction (there are two amino acid and a water
molecule along with substrate forms the reaction center). I want to retain
the bond lengths of partial bands during the charge fitting process.

I will be very thankful if some one can guide me through this charge fitting
process in RED-III.

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Received on Mon Jul 06 2009 - 17:30:25 PDT
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