ADL: Binding affinity contributions

Oleg Trott trott at scripps.edu
Fri Jun 28 17:01:43 PDT 2013


(a) Yes, see the manual, the advanced options.

(b) steric interactions (see the paper)

(c) Yes, but in a different way from AD4 (see the paper).

On Fri, Jun 28, 2013 at 12:08 AM, #SK MAHASIN ALAM#
<SKMA0001 at e.ntu.edu.sg> wrote:
> Dear Friends,
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>
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> I am performing docking study of Cu-complex with G-quadruplex using Autodock Vina. For one of my lignads the calculated binding affinity is -7.5 kcal/mol.
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> (a Is it possible to know the contribulations of hydrophobic, hydrogen bonding etc to the calculated binding affinity in terms of energy, e.g., how much kcal/mol is contributed to -7.5 kcal/mol due to hydrogen bonding?
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> (b) what is the physical meaning of gauss1 and gauss2?
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> (c) Is Vina program considered the electrostatic interactions?
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> Thanks a lot for your kind helps and valuable time.
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> Warm regards
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> Mahasin
> ________________________________________________
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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