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 option. 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 Tehran Iran http://www.ibb.ut.ac.ir/
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