Thanks Case for your comment!
Best wishes
On 3/21/11 7:23 PM, case wrote:
On Mon, Mar 21, 2011, Mahmoud Soliman wrote:
I need to calculate the binding energy for some synthesized ligands in our
lap with some artificial enzyme (which I simulate as well). the problem is
that I notice these ligands does not stick to the protein (as it appear in
X-ray structure that we developed also in our lap) in a free MD simulation.
You won't be able to estimate the binding energies if the bound complex is not
stable in an MD simulation. You *might* use restraints to force binding, and
study resultant snapshots for clues as to why the ligand is not happy in the
binding site.
....dac
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Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
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Mahmoud E. Soliman
Lecturer of pharmaceutical organic chemistry
Pharmaceutical Organic Chemistry Dept.
Faculty of pharmacy
Zagazig University
Zagazig
Egypt
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Email:
[5]mess20.bath.ac.uk
[6]meelkot.zu.edu.eg
[7]mahmoudelkot.gmail.com
References
1. mailto:AMBER.ambermd.org
2.
http://lists.ambermd.org/mailman/listinfo/amber
3.
http://people.bath.ac.uk/mess20/
4.
http://www.bath.ac.uk/person/812559
5. mailto:mess20.bath.ac.uk
6. mailto:meelkot.zu.edu.eg
7. mailto:mahmoudelkot.gmail.com
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Received on Mon Mar 21 2011 - 11:00:02 PDT
