[Dock-fans] Help: How to seperate GB/SA Score to each residue?

[Suhaib Shekfeh]

regarding your last question, I think your interest in GB/SA is beyond the
scope of Dock

to get Free energy decomposition pro residue you have to use Amber software
, PBSA module. I think you should work with Amber if you are so interested
about details of GBSA or PBSA.



On Thu, Mar 26, 2009 at 6:52 AM, thirsty <thirstymail at gmail.com> wrote:

> I got these value from dock.out     but I cannot find any correlative
> information about them
>
> " RECEPTOR
>  GPSELF=-31980.4 GPSHLD=28318.7 SASA=13797.2
>  Total: GB=-3661.73 SA=75.7008 Time=146.188s
> LIGAND
>  GPSELF=-557.713 GPSHLD=360.11 SASA=893.681
>  Total: GB=-197.603 SA=5.76375 Time=1.282s
> COMPLEX
>  GPSELF=-32361.5 GPSHLD=28746.2 SASA=13636.3
>  Total: GB=-3615.23 SA=74.8287 Time=170.547s "
>
> What`s the meaning of GPSELF/GPSHLD?      What`s the different between
> SASA(solvent accessible surface area? ) and SA(surface area?)
>
> If I want to know the GB/SA or Vdw of an appointed residue? What should I
> write in dock.in?
>
> Thank you!
>
> GuanXin
> 2009.03.26
>
>
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>


-- 
Pharmacist. Suhaib Shekfeh
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universität Halle-Wittenberg
Wolfgang-Langenbeck-Str. 4
06120 Halle (Saale), Germany

Tel:    0049 345 55 25 043
Fax:   0049 345 55 27 355
Local Time : GMT + 1
http://pc.pharmazie.uni-halle.de/akmedchem/mitarbeiter/shekfeh/
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