[gmx-users] pdb2gmx on KcsA

Mark Abraham mark.abraham at anu.edu.au
Wed Dec 28 12:36:12 CET 2005

> Did anyone tried to work on this problem earlier, or can anyone suggest
> how
> to deal with this problem of adding missing residues.

One approach is to use some visual molecule builder program to pick a
chemically reasonable starting point for each of the side chains you have
to build and do an energy minimisation on that (preferably restraining the
atoms you haven't fabricated to their positions in the PDB file). You
would want to be intelligent about side chains in active sites or pores or


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