ADL: (no subject)

Michele Lunelli efunit at
Fri Mar 28 08:44:55 PDT 2008

qiaoyan wrote:

> What is the exact meaning by saying "merge the non-polar hydrogen" in
> autodock mannual? Does it means that if there are two hydrogen atoms( one
> polar, the other non-polar ) which are near to each other can be treated as 
> one hydrogen atom 

No, it means that the non-polar hydrogens are deleted from the model, and their 
charge is merged to the charge of the carbon atom which they bind. This is done 
in order to reduce the degrees of freedom of the system, by using a so called 
united-atom force field. From wikipedia: "united-atom force fields treat the 
hydrogen and carbon atoms in methyl and methylene groups as a single interaction 


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