[gmx-users] Hydrogens in lipid bilayer

naga raju nagaraju_cy at yahoo.co.in
Fri Jul 22 14:13:01 CEST 2005

Dear gmx-users,
                I am new user to gromacs. I used
GROMOS96 43a1, GROMOS96 43b1, GROMOS96 43a2 force
field by pdb2gmx command, none of these force field
added all hydrogens to the protein. 

In this site to the lipid bilayer hydrogen atoms are
not present in pdb files as well as in dppc.itp,
lipid.itp files. 
        Does gromacs consider hydrogen atoms in
dynamics calculations. If it consider in calculations
how to get topology files that contains hydrogens.
PRODRG2 server   gives gromacs topology file only for
heavy atoms, how can i get hydrogen containing
topology files.  
     Thank you 

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