Dear Sir or Madam,maybe it sounds a trivial question, yet how I define the phi and psi dihedrals in my topology. I have the section [ dihedrals ] in my topology, yet whenever I try to calculate them via g_chi I get that error :Fatal error: No dihedrals in your structure!and the g_rama command gives no output. In this post : http://www.gromacs.org/pipermail/gmx-users/2005-October/017645.htmlis sais to use a pdb file and write down the numbers of the dihedrals. Yet, this is not the same with what we do in the topology file when we declare the dihedrals? I have used p pdb file as input in the aforementioned command with no luck. The system I have is a polymer one and I do not use any gromacs forcefield. Still, can I use the commands g_chi and g_rama?Yours Sincerely,NIkos
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