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<DIV><FONT face=Arial>Hello all,<BR><BR>I am trying to develop a topology file
for a sugar molecule (with glucose residue linked 1-3) and I have some
questions:</FONT></DIV>
<DIV><FONT face=Arial>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.</FONT></DIV>
<DIV><FONT face=Arial>2. In 'GLCB' residue (in the
ffgmx.rtp file) there are <U>five</U> 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 <U>six</U> ((:-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)</FONT></DIV>
<DIV><FONT face=Arial>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).</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Thank you,<BR>gianfranco</DIV>
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