Hi Gromacs Users, I want to mutate a glutamate in my protein to alanine in presence of a ligand. With glutamate, the protein charge is -3. To neutralize the system, I added 3K+ ions. Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2 + 3K+).
Right now I'm in the charge part of the mutation. Once this is successful, I will include the VDW mutation too. I have added the mutation details of Glu to Ala residue in the topology in [atoms], [bonds], [angles] and [dihedrals] sections. After I run the grompp command, the result says that my State_B topology has +1 charge since I am not including mutation of one K+ ion to neutral K+ ion. How can I mutate 1 particular K+ to K atom and subsequently to a dummy atom? Since I'm using OPLS force field, we have ions.itp to be used in the topology file, changing one K+ is making it troublesome for me to implement in the topology file. Any suggestions are helpful. Thanks for your time. Regards Sai
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