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<DIV><FONT face=Arial size=2> I have some answer to my questions 2 and
3.</FONT></DIV>
<DIV><FONT face=Arial size=2>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</FONT></DIV>
<DIV><FONT face=Arial size=2>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.</FONT></DIV>
<DIV><FONT face=Arial size=2>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.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>sorry for the large number of mistakes in my
previous email. </FONT></DIV>
<DIV><FONT face=Arial size=2>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.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>thank you again</FONT></DIV>
<DIV><FONT face=Arial size=2>gianfranco</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<BLOCKQUOTE dir=ltr
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=gianfranco.bocchinfuso@uniroma2.it
href="mailto:gianfranco.bocchinfuso@uniroma2.it">Gianfranco Bocchinfuso</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Thursday, June 26, 2003 11:54
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] sugar chain</DIV>
<DIV><BR></DIV>
<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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