[gmx-users] change the ligand in pdb file

Rui Li moonfine at mail.sdu.edu.cn
Thu May 10 11:46:34 CEST 2007

Dear Erik and Florian,

Thanks for your reply.In my pdb file, the ligand has has been bound with the 
enzyme(there is a bond between them), and I just want change the side chain of the
ligand, should I use a docking?

On Wednesday, 9. May 2007 10:45, Rui Li wrote:
> Dear all,
>     I want to change the ligand in pdb file(add,delete atoms and change
> conformation),Who can introduce a software to me?
> Any reply is appreciated.Thanks in advance

>As Erik said pymol is a possible solution, but i don`t think that you can 
>easily change conformation of the ligand, for this i would use a docking 
>suite like autodock or something similar, cause you want valid or bioactive 
>conformations of your ligand.



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