[gmx-users] HG at active site of alcohol dehydrogenase

Mahnam mahnam at ibb.ut.ac.ir
Tue May 1 12:05:37 CEST 2007

In God We Trust
Hello Dear GMX users
I want to do MD simulation on alcohol dehydrogenase.When I make topology 
file for this protein , gromacs uses cysH for cys that is connected to Zn in 
 active site. How can I make topology file without HG. 
pdb2gmx doesn't have option for CYS without HG and also I can't use -ss 
I addition I changed HG to DUM and put 0 for its mass, but grompp don't 
accept mass of 0 for this DUM atom.
Many thanks in advance for your help and your reply.
Yours truly 
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384

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