[gmx-users] Dextran Simulations

toma0052 toma0052 at umn.edu
Wed Dec 5 02:14:00 CET 2007

     I would like to simulate the glucose polymer dextran (~5-10 subunits)
and I am wondering what is the best way to do go about doing this.  In
looking at ffgmx.rtp I see GLCA/B which seem to be the glucose parameter
files.  If my numbering scheme is correct, to produce a linear dextran
molecule I want alpha(1-6) linkages, or alpha(1-4) linkages for a branched
polymer which would correspond to O6-C1 and O3-C1 respectively.  However, in
the .rtp file, these bonds are not given, only O4-C1 and O2-C1 are included. 
Is my numbering off, or is there another way to do this?
     I have tried the PRODRG server to create these molecules, and it seemed
to work alright, but I am still a little skeptical about the output.  The
charges appear to be different than in the ffgmx.
     I understand that ffgmx is depreciated, which leads to me second
question (Maybe this should be a different thread).  I would like,
eventually, to look at the different dextran polymers interacting with a DPPC
bilayer.  For the lipids, I am using those of Dr. P. Tieleman in which my
dppc.top file includes ffgmx.itp which is why I am looking at this force
field for the dextran.  If ffgmx is not a force field to use, what would be
better for simulating lipids and carbohydrates?  ffG43a2x?  I have read for
protein simulations people using the Berger lipids and OPLS-AA, would it be
fair to extend this to lipids and carbohydrates?

Mike Tomasini

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