[gmx-users] building a beta-glucose chain

Glenn Johnson gjohnson at srrc.ars.usda.gov
Wed Dec 15 00:08:53 CET 2004

I would like to run some simulations of cellulose with Gromacs but am
running into some difficulty.  I am a newbie to Gromacs so that is no
doubt a factor.  I have a 4 beta-glucose residue chain (1->4 linkage)
that I am starting with.  I hand edited the PDB file to correspond to
the atom names, etc. in the ffG43a1.rtp file.  First off, I am not sure
if the GLCA building block is the correct one to use.  It is for a 1->4
linkage but for alpha-glucose.  Anyway, I was able to build a topology
file for my structure.  However, I do not see any terms for the bond
lengths, bond angles, and dihedrals between the residues in the topology
file.  Upon energy minimization, the residues simply move away from each
other at the points where they are supposed to be bonded.  I am
attaching my PDB file.  Perhaps someone can see what I have wrong.


Glenn Johnson <gjohnson at srrc.ars.usda.gov>
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