Dear gmx-users,<br>                       I&#39;m having some problems using the flag &quot;-ter&quot; of pdb2gmx.<br>The syntax I&#39;m using is the following, for a protein dimer:<br>                     <br>                     pdb2gmx -f protein_dimer.pdb -o start.gro -p start.top -ter<br>
<br>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.<br><br>What I&#39;m attempting to do is to create a C-terminus without a carboxylic group.<br>
Best regards<br>                                                                                                                                   Alberto<br><br><br><br>