[gmx-users] H2 topology

011013021-Jyotsna 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 dummy)
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 

Thank You,

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