[gmx-users] topology for c-alpha protein model

Diego Nolasco nolasco1980 at gmail.com
Fri Jun 20 19:36:19 CEST 2008

After pdb2gmx of the whole structure, make an index file and them run
another pdb2gmx choosing the c-alpha group. I hope it helps.

2008/6/20, Lillian Chong <ltchong42 at gmail.com>:
> Dear Gromacs Users,
> I would like to generate a topology for a protein in which each
> residue is represented only by its C-alpha atom (a Go-type model).
> What would be the most straightforward way of creating this topology
> file?
> Thanks in advance,
> Lillian
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