[gmx-users] [Fwd: Topology for sugar molecules!]

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 11 12:48:40 CEST 2005

-------- Forwarded Message --------
From: Somer Bekiroglu <somer at organ.su.se>
Reply-To: somer at organ.su.se
To: spoel at xray.bmc.uu.se
Subject: Topology for sugar molecules!
Date: Mon, 11 Apr 2005 12:41:25 +0200

I want to use Gromacs for MD on some disaccharides in explicit water box. The 
problem I encounter is that my molecules do not exist in the databases of 
Gromacs so that pdb2gmx would produce the necessary top files. I also tried  
"The Dundee PRODRG2 Server" to get the topologies. Unfortunately it only 
produces topologies where hydrogens sitting on carbons are condensed on 
carbon atoms they sit on. I need them explicitly since I would like to partly 
study the NMR coupling contanst of hydroxy protons and C-H protons. I mean 
3J(H-O-C-H). So my questions are;

1- Are the force fields that are implemented in Gromacs capable of taking care 
of hydrogens sitting on carbon atoms in a sugar molecule explicitly?

2- How can I most reliably produce topologies for my disaccharides that will 
be placed in a water box to perform MD?

I am quite new to MD methods therefore I apologize already now if I put 
forward something incoherent.

Thanks for the help,


David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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