[gmx-users] H2 topology

011013021-Jyotsna 011013021 at bioinfo.sastra.edu
Mon Feb 1 10:57:58 CET 2010

Dear all,

I want to run a simulation for an enzyme. It demands me to 
incorporate a Molecular hydrogen Topology with a dummy 
atom in between in the simulation in order to study the 
path of hydrogen in it.The problem is , the topology file 
I built induces many errors when i come to the energy 
minimization step. The version of gromacs I am using is 
4.0. The topology file I built is as follows

[ moleculetype ]
;name    nrexcl
   H2       3

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr 
       charge     mass    ; total charge
      1     H       1     H2        H1      1 
          0.475    1.00800  ; 0.00
      2     H       1     H2        H2      1 
          0.475    1.00800  ; 0.00
      3     DUM     1     H2        DUM     1 
         -0.950    0.000

[ virtual_sites2 ]
; Site from funct a
3 1 2 1 0.7439756

When ever I insert the hydrogen+dummy atom topology in the 
protein's .gro file, an error is generated regarding 
mismatch of residues or the dummy atom having mass 0 .

I would be really grateful if anyone could provide me the 
hydrogen molecule topology and give some pointers towards 

Thank you,


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