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

[David van der Spoel]

-------- 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
Hi,

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,

Somer


-- 
David.
________________________________________________________________________
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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