ADL: (no subject)

qiaoyan qiaoyan at
Fri Mar 28 07:16:54 PDT 2008

Dear all,  


  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, e.g

 -C-N-HN , then HN and HC can be treated as 




one hydrogen atom as  -C-N-HN ?

                       |  /

                       | /




    I used the ADT to prepare my pdb files and to generate rec_rigid.pdbqt
file. But I noticed some strage bonds as above in the sidechain of LYS and


Any suggestion is greatly appreciated.


Thanks for the time.


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