[gmx-users] sugar chain

Gianfranco Bocchinfuso gianfranco.bocchinfuso at uniroma2.it
Fri Jun 27 16:34:00 CEST 2003

 I have some answer to my questions 2 and 3.
1.         in the glucose there are only five equatorial atoms and not six as I said, then we need five improper dihedrals, as it is in the GLCB residue in the ffgmx.rtp file
2.        one of the five improper dihedral in my rtp residue was not correct, and this is the reason because pdb2gmx generates the 6th improper angle.
3.         I don't need to set 1-4 interaction if I define a new improper dihedral, simply because there are not 1-4 atoms in an improper-dihedral angle.

sorry for the large number of mistakes in my previous email. 
The only reasonable question it is just the first one in my previous email, at present I set the 'angletypes' parameter for similarity with other angles defined in the ffgmxbon.itp file. If someone has a better solution please give me notice.

thank you again

  ----- Original Message ----- 
  From: Gianfranco Bocchinfuso 
  To: gmx-users at gromacs.org 
  Sent: Thursday, June 26, 2003 11:54 AM
  Subject: [gmx-users] sugar chain

  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,

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