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. Andrea
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