[gmx-users] Automating pdb2gmx

Jernej Zidar jernej.zidar at gmail.com
Wed Nov 4 02:17:28 CET 2015

  I would like to import several hundred molecules to Gromacs.

  I know that one can set the force field "automatically" and pick the
desired water model like so:
echo 16 | pdb2gmx -f some.pdb -water spc

  Is there a way to automate the selection of the termini? The proteins I
am importing have no termini, i.e. when prompted I have to pick "3" for
both N- and C-terminals of both chains, however I can't see an option to do
that "automatically".

  Any tips on how to do that?


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