[gmx-users] sugar chain
spoel at xray.bmc.uu.se
Fri Jun 27 17:11:01 CEST 2003
On Fri, 2003-06-27 at 16:32, Gianfranco Bocchinfuso wrote:
> 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.
The force constant is not crucially important but the angles are. Do
also check what happens to a single ring after minimization (i.e. 1-4
interactions may screw up your conformation).
> 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,
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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