[gmx-users] sugar chain

David 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
> gianfranco
>         ----- 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,
>         gianfranco
Groeten, David.
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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