[AMBER] stacking energy calculation

From: hari krishna <haricoolguy111.gmail.com>
Date: Wed, 16 Mar 2011 15:36:36 +0530

Hi all:

      Initially I did a simulation for 20ns for a DNA and ligand system. I
want to calculate the stacking energy between the Ligand and DNA, I removed
the atoms of backbone and bases except the bases contributing to the
stacking with the ligand. Then I calculated the sinlge point energy using
the Gaussian, how can i remove the energy contributed from electrostatics or
H-bond except from stacking energy. Is there is any way to calcluate using
the MD trajectory files from simulation.

HariKrishna. S
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Received on Wed Mar 16 2011 - 03:30:08 PDT
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