Gromacs Users,
The Onuchic Group at UCSD has developed a webtool and tutorial for
using All-atom (and C-alpha) Structure-based Hamiltonians (aka Go Models) in
Gromacs. http://sbm.ucsd.edu/ All you need to do is provide a pdb file
with protein, RNA and/or DNA chains (there are also some supported ligands)
and the webtool will provide you with the appropriate .gro and .top files.
Basically, this module does what pdb2gmx does, but for structure-based
forcefields. It is only "beta" because we periodically add more
functionality to the tool. We already use the tool to prepare production
simulations. Questions, comments and suggestions regarding this model and
webtool should be directed to [email protected], and not the gmx-users
list.
Hope you find this resource useful.
Paul Whitford
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