[gmx-users] extract dihedrals from ALAD.pdb

Antonia Mey ppxasjsm at nottingham.ac.uk
Mon Dec 17 16:05:43 CET 2012

I am trying to simulate alanine dipeptide with the CHARMM27 force field
I have downloaded the ALAD file provided here:


And the run pdb2gmx, solvation, minimization and nvt equilibration
Everything worked fine, but when I want to use g_rama to extract the dihedral angle pairs, none are found.
how and where do I need to add the information manually so that the dihedral phi and psi pair around 5 7 9 15 and 7 9 15 17 is found?

Adding the following line to the topology file did not solve the problem:
[ dihedrals]

  5      7     9     15     1
  7      9     15    17     1

Any help would be greatly appreciated!

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