[gmx-users] topology

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 10 06:12:49 CET 2008

naimah haron naimah wrote:
> Dear all...
> How to draw the structure for ionic liquid and get their PDB file? For 
> example, we can draw the struture by using PRODRG generation server and 
> get their PDB file. So, any suggestion to draw the structure and get 
> their PDB file without using PRODRG generation server?

Build a small one by hand in a text editor (making sure the density is 
suitable and there won't be steric clashes across periodic boundaries), 
replicate it with genbox, and equilibrate.


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