[gmx-users] Dihedral not counted?

Andrea Muntean andreamuntean at gmail.com
Mon Oct 27 15:53:29 CET 2008

Hi all,

I defined my residues for Polystyrene (first, last and inner monomers), with
the coresponding bonds, angles, dihedrals and impropers, including also the
conectivities (as + and - atoms of the next or previous residue). Pdb2gmx
runs without error or warning, but it counts less dihedrals then I would
expect. I did run the same for dimer and trimer. For dimer is ok, for trimer
starts to count 1 dihedral less, and for the chain with 80 monomers
corespondingly 78 dihedrals less, which means that the error should be in
the inner residue. I checked many times, but the dihedral which is missing
in the .top file is defined in the .rtp. So I have really no clue what is
wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me.

Please give me a good idea :o)

Thanks in advance.
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