ADL: Binding affinity contributions

Oleg Trott trott at scripps.edu
Thu Jul 11 14:53:57 PDT 2013


I think Eq. 9 in the paper is what you are looking for.

On Thu, Jul 11, 2013 at 2:30 AM, #SK MAHASIN ALAM#
<SKMA0001 at e.ntu.edu.sg> wrote:
> 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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>
> ________________________________________________
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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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