[gmx-users] sugar chain

[Gianfranco Bocchinfuso]

Hello all,

I am trying to develop a topology file for a sugar molecule (with glucose residue linked 1-3) and I have some questions:
1.     in the ffgmx.rtp file there is two glucose residue, but in the ffgmxbon.itp there is not parameter for four angles (for example os-cs1-os1) of the glucose ring.
2.      In 'GLCB' residue (in the ffgmx.rtp file) there are five improper dihedral (are they sufficient to preserve six equatorial atoms?), that I use when I create the topology for my molecule (in the rtp file); when pdb2gmx creates the file *.top it writes six ((:-o)) improper dihedrals per residue, and the 6th angle (that is in the improper dihedral section of the .top file) it is really an proper dihedral (it is the o2-c2-ci-o5 angle in the ring)
3.     last (more general ) question, if I define this improper dihedral, I have to define also the 'pairs' parameter between 1-4 atoms (o2 and o5 atoms in my system).

Thank you,
gianfranco


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