[gmx-users] H2 topology
011013021 at bioinfo.sastra.edu
Wed Feb 3 07:52:55 CET 2010
Dear Justin ,
Thank you very much for your help.
To create a linear H2 molecule with a dummy atom in the
center is proving to be quite a difficult task.
Hence , I created a pdb file of CO2 using Cerius(2) , and
replaced the atoms in the pdb file with 2 H atoms and a
dummy atom.(since CO2 is a three atom , linear system i.e
the two O atoms replaced by two H atoms and the C atom by
The problem is the bond distance. For CO2 , it is 1.66 A
but I need the distance for H2 to be only 0.7 A as per the
literature I am following. By replacing the atoms in the
pdb file , there is a problem regarding distance since the
coordinates of the pdb also point towards 1.6 A.
I would be very grateful if you could tell me how I can
build a PDB for H2 with dummy atom with the right
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