[gmx-users] GLY dihedrals in amber03 family force fields

Tomek Wlodarski tomek.wlodarski at gmail.com
Wed Oct 29 13:36:00 CET 2014


I looked into amber03w topology file for amino acids and I found that GLY
has interesting dihedral defined:

    -C     N    CA    CB

Which gives me warnings with pdb2gmx:

WARNING: WARNING: Residue 75 named GLY of a molecule in the input file was
to an entry in the topology database, but the atom CB used in
an interaction of type dihedral in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be

I looked into amber03 main paper but I have not found anything related...
Any idea why this dihedral is defined for GLY?


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