ADL: Binding affinity contributions

#SK MAHASIN ALAM# SKMA0001 at e.ntu.edu.sg
Thu Jul 11 02:30:55 PDT 2013


Dear Sir,

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.

Warm regards

Mahasin
________________________________________ 
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
>
>
>
> 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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