[gmx-users] the ligang topology

Jianguo Li ljggmx at yahoo.com.sg
Thu Feb 16 03:07:01 CET 2012

This paper has used united atoms for -CF3 and -CF2: 

Hiroaki et al. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study. J. Phys. Chem. B 2008, 112, 11305–11309.

Another way is to use ATB to generate the topology, but I am not sure if it can deal with fluorine atom. http://compbio.biosci.uq.edu.au/atb/ 


 From: xiaojiong <xiaojiong at zju.edu.cn>
To: gmx-users at gromacs.org 
Sent: Wednesday, 15 February 2012, 19:35
Subject: [gmx-users] the ligang topology 

    The topology for my ligand was created employing the server PRODRG 2.5 Beta. Now I change the charges to consistent with the GROMOS96,but I don't know the charges of -CF3 and C-Cl .Where can I find or can you tell me?Thanks!

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