Dear friends
I am trying to run a MD simulation with a Zn ion in the
active site. The zinc makes covalent bond to His , Asp , Cys and Drug
molecule. however I am trying to study various ligands that make a
sustainable bond with zn over period of time. I am new to gmx and I am
pretty confused with .rtp and specbond.dat . How should I make His (its
actually HisD) , Asp and Cys bonded with Zn and enough residual charge on zn
with which it can form a bond to ligand molecule. will definitions of bond
lengths and bond angles on specbond.dat will alone suffice ? I am using
Amber99sb ff so that I can carry out md on my fermi card. any help is highly
appreciated.
thanks and regards
bharath
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