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/
Jianguo
________________________________
From: xiaojiong <xiaoji...@zju.edu.cn>
To: gmx-users@gromacs.org
Sent: Wednesday, 15 February 2012, 19:35
Subject: [gmx-users] the ligang topology
Dear,
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!
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
