ADL: Binding affinity contributions
#SK MAHASIN ALAM#
SKMA0001 at e.ntu.edu.sg
Thu Jul 11 02:30:55 PDT 2013
For configuartion 1, I have obtained the following intermolecular terms using the advanced options
gauss 1 : 99.91680
gauss 2 : 1269.16837
repulsion : 1.05184
hydrophobic : 6.02995
Hydrogen : 0.89073
The weights are (from the paper)
gauss 1 : -0.0356
gauss 2 : -0.00516
repulsion : 0.840
hydrophobic : -0.0351
Hydrogen : -0.587
My question is how to convert this to energy? Is it the multiplication of Intermolecular terms and their weights?
If this is the case, the summation of (terms x weights) is -9.96, however, the binding affinity for this configuration is -7.52 kcal/mol.
Please help me how to convert the intermolecular terms to energy. Thanks a lot for your help and valuable time.
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on behalf of Oleg Trott [trott at scripps.edu]
Sent: Saturday, 29 June, 2013 8:01:43 AM
To: autodock at scripps.edu
Subject: Re: ADL: Binding affinity contributions
(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,
> 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.
> (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?
> (b) what is the physical meaning of gauss1 and gauss2?
> (c) Is Vina program considered the electrostatic interactions?
> Thanks a lot for your kind helps and valuable time.
> Warm regards
> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
Oleg Trott, Ph.D. (Columbia University)
Staff Scientist in the Olson Lab
The Scripps Research Institute
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