[gmx-users] -ter flag, pdb2gmx

alberto arrigoni arrigonialberto86 at gmail.com
Tue Nov 22 15:17:43 CET 2011

Dear gmx-users,
                       I'm having some problems using the flag "-ter" of
The syntax I'm using is the following, for a protein dimer:

                     pdb2gmx -f protein_dimer.pdb -o start.gro -p start.top

Instead of prompting a menu with the choice of different chemical groups,
the flag is ignored by gromacs, which creates the ouput files as usual.

What I'm attempting to do is to create a C-terminus without a carboxylic
Best regards

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