[gmx-users] making topology file for infinite crystal

Vishal Agarwal vishal.iitian at gmail.com
Sun Feb 7 04:52:15 CET 2010

Dear All,

Can anyone help me how can I go about preparing the topology file for an
infinite crystal of cellulose. I have prepared the .gro file for 5X5X5 unit
cells of cellulose II using GROMACS utility and intend to apply periodic BC
on it. It has a glucose molecule as building block (GCLA). When I try
running pdbgmx, I get an error for extra hydrogens (which is not there in
itp file but is actually there in the original structure which I am using)
and missing oxygen (-O).


Vishal Agarwal
Research Scholar
University of Massachusetts, Amherst
'Your only obligation in any lifetime is to be true to yourself."
            ---Richard Bach
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